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

examples/example_InputDeck.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,73 +38,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "Parsing input deck : example_data/thermal.1d\n",
-      "Reading simulation\n",
-      "  random_seed = 0\n",
-      "  wall_clock_limit = \"23:50:00\"\n",
-      "  wall_clock_check = 2000\n",
-      "  wall_clock_checkpoint = .true.\n",
-      "Reading node_conf\n",
-      "  node_number(1:1) = 4\n",
-      "  if_periodic(1:1) = .true.\n",
-      "Reading grid\n",
-      "  nx_p(1:1) = 500\n",
-      "  coordinates = \"cartesian\"\n",
-      "Reading time_step\n",
-      "  dt = 0.0099\n",
-      "  ndump = 1\n",
-      "Reading restart\n",
-      "  if_restart = .false.\n",
-      "Reading space\n",
-      "  xmin(1:1) = 0.\n",
-      "  xmax(1:1) = 5.0\n",
-      "  if_move(1:1) = .false.\n",
-      "Reading time\n",
-      "  tmin = 0.0d0\n",
-      "  tmax = 2.5\n",
-      "Reading el_mag_fld\n",
-      "Reading emf_bound\n",
-      "  type(1:2,1) = \"open\",\"open\"\n",
-      "Reading diag_emf\n",
-      "  ndump_fac = 1\n",
-      "  ndump_fac_ene_int = 1\n",
-      "  reports = \"e1\",\"e2\",\"e3\"\n",
-      "Reading particles\n",
-      "  interpolation = \"linear\"\n",
-      "  num_species = 1\n",
-      "Reading species\n",
-      "  name = \"electrons\"\n",
-      "  num_par_max = 2048\n",
-      "  rqm = -1.0\n",
-      "  num_par_x(1:1) = 64\n",
-      "Reading udist\n",
-      "  uth_type = \"thermal\"\n",
-      "  uth(1:3) = 0.01,0.01,0.01\n",
-      "Reading profile\n",
-      "  density = 1\n",
-      "  profile_type = \"uniform\"\n",
-      "Reading spe_bound\n",
-      "Reading diag_species\n",
-      "  ndump_fac_ene = 1\n",
-      "  ndump_fac_temp = 1\n",
-      "  ndump_fac = 1\n",
-      "  reports = \"charge\"\n",
-      "  rep_udist = \"vfl1\",\"T11\"\n",
-      "Reading smooth\n",
-      "Reading diag_current\n",
-      "Input deck successfully parsed\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "deck = ou.InputDeckIO('example_data/thermal.1d', verbose=True)"
    ]
@@ -123,19 +59,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Simulation Dimensions: 1\n",
-      "Number of species: 1\n",
-      "Species: {'electrons': Specie(name=electrons, rqm=-1.0, q=-1.0, m=1.0)}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(\"Simulation Dimensions:\", deck.dim)\n",
     "print(\"Number of species:\", deck.n_species)\n",
@@ -155,19 +81,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['simulation', {'random_seed': '0', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n",
-      "['node_conf', {'node_number(1:1)': '4', 'if_periodic(1:1)': '.true.'}]\n",
-      "Number of sections: 18\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(deck.sections[0])\n",
     "print(deck.sections[1])\n",
@@ -187,18 +103,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[{'random_seed': '0', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n",
-      "[{'node_number(1:1)': '4', 'if_periodic(1:1)': '.true.'}]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(deck['simulation'])\n",
     "print(deck['node_conf'])"
@@ -213,18 +120,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "0\n",
-      "0\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# this one returns a list since there can be multiple sections with the same name\n",
     "print(deck.get_param(section='simulation', param='random_seed')[0])\n",
@@ -245,18 +143,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Before [{'random_seed': '0', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n",
-      "After [{'random_seed': '42', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# edit a parameter already exists\n",
     "print('Before', deck['simulation'])\n",
@@ -266,18 +155,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Before [{'random_seed': '42', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n",
-      "After [{'random_seed': '42', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.', 'new_parameter': '\"HI!\"'}]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# add a parameter\n",
     "print(\"Before\", deck[\"simulation\"])\n",
@@ -294,18 +174,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Before [{'random_seed': '42', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.', 'new_parameter': '\"HI!\"'}]\n",
-      "After [{'random_seed': '42', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# delete a parameter\n",
     "print(\"Before\", deck[\"simulation\"])\n",
@@ -328,19 +199,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Before [{'random_seed': '42', 'wall_clock_limit': '\"23:50:00\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n",
-      "After 1 [{'random_seed': '#tag#', 'wall_clock_limit': '\"#tag#\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n",
-      "After 2 [{'random_seed': 'BOTH CHANGED', 'wall_clock_limit': '\"BOTH CHANGED\"', 'wall_clock_check': '2000', 'wall_clock_checkpoint': '.true.'}]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# this a dummy example where we change some values to #tag#\n",
     "print(\"Before\", deck[\"simulation\"])\n",
@@ -373,123 +234,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "simulation\n",
-      "{\n",
-      "\trandom_seed = BOTH CHANGED,\n",
-      "\twall_clock_limit = \"BOTH CHANGED\",\n",
-      "\twall_clock_check = 2000,\n",
-      "\twall_clock_checkpoint = .true.,\n",
-      "}\n",
-      "\n",
-      "node_conf\n",
-      "{\n",
-      "\tnode_number(1:1) = 4,\n",
-      "\tif_periodic(1:1) = .true.,\n",
-      "}\n",
-      "\n",
-      "grid\n",
-      "{\n",
-      "\tnx_p(1:1) = 500,\n",
-      "\tcoordinates = \"cartesian\",\n",
-      "}\n",
-      "\n",
-      "time_step\n",
-      "{\n",
-      "\tdt = 0.0099,\n",
-      "\tndump = 1,\n",
-      "}\n",
-      "\n",
-      "restart\n",
-      "{\n",
-      "\tif_restart = .false.,\n",
-      "}\n",
-      "\n",
-      "space\n",
-      "{\n",
-      "\txmin(1:1) = 0.,\n",
-      "\txmax(1:1) = 5.0,\n",
-      "\tif_move(1:1) = .false.,\n",
-      "}\n",
-      "\n",
-      "time\n",
-      "{\n",
-      "\ttmin = 0.0d0,\n",
-      "\ttmax = 2.5,\n",
-      "}\n",
-      "\n",
-      "el_mag_fld\n",
-      "{\n",
-      "}\n",
-      "\n",
-      "emf_bound\n",
-      "{\n",
-      "\ttype(1:2,1) = \"open\", \"open\",\n",
-      "}\n",
-      "\n",
-      "diag_emf\n",
-      "{\n",
-      "\tndump_fac = 1,\n",
-      "\tndump_fac_ene_int = 1,\n",
-      "\treports = \"e1\", \"e2\", \"e3\",\n",
-      "}\n",
-      "\n",
-      "particles\n",
-      "{\n",
-      "\tinterpolation = \"linear\",\n",
-      "\tnum_species = 1,\n",
-      "}\n",
-      "\n",
-      "species\n",
-      "{\n",
-      "\tname = \"electrons\",\n",
-      "\tnum_par_max = 2048,\n",
-      "\trqm = -1.0,\n",
-      "\tnum_par_x(1:1) = 64,\n",
-      "}\n",
-      "\n",
-      "udist\n",
-      "{\n",
-      "\tuth_type = \"thermal\",\n",
-      "\tuth(1:3) = 0.01, 0.01, 0.01,\n",
-      "}\n",
-      "\n",
-      "profile\n",
-      "{\n",
-      "\tdensity = 1,\n",
-      "\tprofile_type = \"uniform\",\n",
-      "}\n",
-      "\n",
-      "spe_bound\n",
-      "{\n",
-      "}\n",
-      "\n",
-      "diag_species\n",
-      "{\n",
-      "\tndump_fac_ene = 1,\n",
-      "\tndump_fac_temp = 1,\n",
-      "\tndump_fac = 1,\n",
-      "\treports = \"charge\",\n",
-      "\trep_udist = \"vfl1\", \"T11\",\n",
-      "}\n",
-      "\n",
-      "smooth\n",
-      "{\n",
-      "}\n",
-      "\n",
-      "diag_current\n",
-      "{\n",
-      "}\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "deck.print_to_file(\"edited-deck.1d\")\n",
     "! cat edited-deck.1d"
@@ -498,7 +245,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "tese-env",
+   "display_name": "plasma",
    "language": "python",
    "name": "python3"
   },
@@ -512,7 +259,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,

examples/example_Simulation_Diagnostic.ipynb

@@ -6,10 +6,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import osiris_utils as ou\n",
-    "import numpy as np\n",
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "import matplotlib.pyplot as plt\n",
-    "from matplotlib.colors import LogNorm"
+    "import numpy as np\n",
+    "\n",
+    "import osiris_utils as ou"
    ]
   },
   {
@@ -68,7 +78,7 @@
     "# e3 is a Diagnostic object\n",
     "e3 = ou.Diagnostic(\"example_data\", \"electrons\")\n",
     "# now we need to load the data\n",
-    "e3.get_quantity(\"e3\") # it knows the path there since OSIRIS always saves the data in the same way\n",
+    "e3.get_quantity(\"e3\")  # it knows the path there since OSIRIS always saves the data in the same way\n",
     "\n",
     "print(\"Diagnostic: (e3)\")\n",
     "print(e3)\n",
@@ -118,7 +128,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim[\"e3\"] # This is equivalent to e3\n",
+    "sim[\"e3\"]  # This is equivalent to e3\n",
     "\n",
     "print(sim[\"e3\"])\n",
     "print(sim[\"e3\"].__dict__.keys())"
@@ -137,8 +147,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(sim[\"e3\"][100].shape) # nx\n",
-    "print(e3[100].shape)        # nx\n",
+    "print(sim[\"e3\"][100].shape)  # nx\n",
+    "print(e3[100].shape)  # nx\n",
     "\n",
     "print(\"Are they the same?\", np.isclose(sim[\"e3\"][100], e3[100]).all())"
    ]
@@ -158,7 +168,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(12,4))\n",
+    "plt.figure(figsize=(12, 4))\n",
     "plt.subplot(121)\n",
     "plt.plot(sim[\"e3\"].x, sim[\"e3\"][100], label=\"Simulation\", c=\"tab:orange\")\n",
     "plt.title(\"Using Simulation\")\n",
@@ -200,7 +210,7 @@
     "sim[\"e3\"].load_all()\n",
     "\n",
     "# now, the data is loaded in memory\n",
-    "print(sim[\"e3\"].data.shape) # (n_steps, nx)\n",
+    "print(sim[\"e3\"].data.shape)  # (n_steps, nx)\n",
     "\n",
     "sim[\"e3\"].unload()"
    ]
@@ -220,7 +230,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sum_of_diag = sim[\"electrons\"][\"T11\"] + sim[\"electrons\"][\"vfl1\"] \n",
+    "sum_of_diag = sim[\"electrons\"][\"T11\"] + sim[\"electrons\"][\"vfl1\"]\n",
     "\n",
     "print(sum_of_diag)\n",
     "print(sum_of_diag.__dict__.keys())"
@@ -241,7 +251,7 @@
    "source": [
     "# we can load all the data at once\n",
     "sum_of_diag.load_all()\n",
-    "print(sum_of_diag.data.shape) # (n_steps, nx)\n",
+    "print(sum_of_diag.data.shape)  # (n_steps, nx)\n",
     "sum_of_diag.unload()"
    ]
   },
@@ -258,7 +268,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(12,4))\n",
+    "plt.figure(figsize=(12, 4))\n",
     "plt.subplot(121)\n",
     "plt.plot(sum_of_diag.x, sum_of_diag[100], label=\"T11 + vfl1\", c=\"tab:orange\")\n",
     "plt.title(\"Diagnostic from sum of two diagnostics\")\n",
@@ -280,7 +290,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nT = -1*sim[\"electrons\"][\"T11\"]*sim[\"electrons\"][\"charge\"] # -1 because we are dealing with electrons"
+    "nT = -1 * sim[\"electrons\"][\"T11\"] * sim[\"electrons\"][\"charge\"]  # -1 because we are dealing with electrons"
    ]
   },
   {
@@ -289,7 +299,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(6,4))\n",
+    "plt.figure(figsize=(6, 4))\n",
     "plt.plot(nT.x, nT[100], label=r\"$n_eT_{11}$\", c=\"tab:green\")\n",
     "plt.title(r\"$n_eT_{11}$\")\n",
     "plt.xlabel(nT.axis[0][\"plot_label\"])\n",
@@ -313,7 +323,7 @@
     "sim[\"electrons\"][\"vfl1\"].load_all()\n",
     "sim[\"electrons\"][\"charge\"].load_all()\n",
     "\n",
-    "v_times_charge = sim[\"electrons\"][\"vfl1\"]*sim[\"electrons\"][\"charge\"]\n",
+    "v_times_charge = sim[\"electrons\"][\"vfl1\"] * sim[\"electrons\"][\"charge\"]\n",
     "\n",
     "print(v_times_charge)\n",
     "print(v_times_charge.__dict__.keys())"
@@ -357,7 +367,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "tese-env",
+   "display_name": "plasma",
    "language": "python",
    "name": "python3"
   },
@@ -371,7 +381,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.14.2"
   }
  },
  "nbformat": 4,

examples/quick_start.ipynb

@@ -1,5 +1,16 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cd01bded",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -24,8 +35,10 @@
    "source": [
     "import sys\n",
     "from pathlib import Path\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
-    "import osiris_utils as ou"
+    "\n",
+    "import osiris_utils as ou\n"
    ]
   },
   {
@@ -75,6 +88,9 @@
    "cell_metadata_filter": "-all",
    "formats": "ipynb,py",
    "main_language": "python"
+  },
+  "language_info": {
+   "name": "python"
   }
  },
  "nbformat": 4,

osiris_utils/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from importlib import metadata as _meta
 
 try:
@@ -7,6 +9,7 @@ except _meta.PackageNotFoundError:  # package is being run from a checkout
     # Fallback for `pip install -e .` or direct source use
     __version__ = "0.0.0.dev0"
 
+
 from .data.data import (
     OsirisData,
     OsirisGridFile,
@@ -17,7 +20,7 @@ from .data.data import (
 from .data.diagnostic import Diagnostic
 from .data.simulation import Simulation, Species_Handler
 from .decks.decks import InputDeckIO
-from .decks.species import Specie
+from .decks.species import Species
 from .postprocessing.derivative import Derivative_Diagnostic, Derivative_Simulation
 from .postprocessing.fft import FFT_Diagnostic, FFT_Simulation
 from .postprocessing.field_centering import (
@@ -34,14 +37,15 @@ from .postprocessing.mft import (
     MFT_Diagnostic_Fluctuations,
     MFT_Simulation,
 )
-from .postprocessing.mft_for_gridfile import MFT_Single
 from .postprocessing.postprocess import PostProcess
 from .postprocessing.pressure_correction import (
     PressureCorrection_Diagnostic,
     PressureCorrection_Simulation,
 )
 from .utils import (
+    convert_tracks,
     courant2D,
+    create_file_tags,
     filesize_estimation,
     integrate,
     read_data,
@@ -62,7 +66,7 @@ __all__ = [
     "Diagnostic",
     "Species_Handler",
     # Decks
-    "Specie",
+    "Species",
     "InputDeckIO",
     # PostProcessing
     "PostProcess",
@@ -80,14 +84,14 @@ __all__ = [
     "PressureCorrection_Diagnostic",
     "HeatfluxCorrection_Simulation",
     "HeatfluxCorrection_Diagnostic",
-    # Single file MFT
-    "MFT_Single",
     # Utilities
+    "courant2D",
     "time_estimation",
     "filesize_estimation",
     "transverse_average",
     "integrate",
     "save_data",
     "read_data",
-    "courant2D",
+    "convert_tracks",
+    "create_file_tags",
 ]

osiris_utils/cli/__init__.py

@@ -0,0 +1,6 @@
+"""CLI subcommands for osiris_utils."""
+
+from . import export, info, plot, validate
+from .__main__ import main
+
+__all__ = ["info", "export", "plot", "validate", "main"]