osiris-utils 1.2.0__tar.gz → 1.2.2__tar.gz

{osiris_utils-1.2.0/osiris_utils.egg-info → osiris_utils-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.2.0
+Version: 1.2.2
 Summary: Utilities to manipulate and visualise OSIRIS plasma PIC output data
 Author-email: João Pedro Ferreira Biu <joaopedrofbiu@tecnico.ulisboa.pt>
 License: MIT
@@ -43,6 +43,11 @@ Dynamic: license-file
 
 OSIRIS_UTILS
 ============
+.. image:: https://raw.githubusercontent.com/joaopedrobiu6/osiris_utils/main/docs/source/_static/Imagem1.png
+   :width: 200px
+   :align: right
+
+
 |Pypi|
 
 .. image:: https://github.com/joaopedrobiu6/osiris_utils/actions/workflows/ci.yml/badge.svg
@@ -158,3 +163,4 @@ Contributors
 - Diogo Carvalho
 - João Cândido
 - Margarida Pereira
+

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/README.rst

@@ -1,5 +1,10 @@
 OSIRIS_UTILS
 ============
+.. image:: https://raw.githubusercontent.com/joaopedrobiu6/osiris_utils/main/docs/source/_static/Imagem1.png
+   :width: 200px
+   :align: right
+
+
 |Pypi|
 
 .. image:: https://github.com/joaopedrobiu6/osiris_utils/actions/workflows/ci.yml/badge.svg
@@ -115,3 +120,4 @@ Contributors
 - Diogo Carvalho
 - João Cândido
 - Margarida Pereira
+

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/_static/custom.css

@@ -1,6 +1,7 @@
 /* Sidebar background */
 .wy-nav-side {
-  background: #88cbf8;  /* Change to your preferred color */
+  background: #88cbf8;
+  /* Change to your preferred color */
 }
 
 /* Sidebar link color */
@@ -18,12 +19,17 @@
   background: #2f93f0;
 }
 
-.wy-menu-vertical li.current > a {
+.wy-menu-vertical li.current>a {
   background: #aeecff;
 }
 
 /* Header (H1, H2, etc.) colors */
-h1, h2, h3, h4, h5, h6 {
+h1,
+h2,
+h3,
+h4,
+h5,
+h6 {
   color: #57bafb;
 }
 
@@ -43,11 +49,21 @@ a:hover {
 
 /* Keep your existing table width overrides */
 @media screen and (min-width: 767px) {
-.wy-table-responsive table td {
-  white-space: normal !important;
-}
+  .wy-table-responsive table td {
+    white-space: normal !important;
+  }
 
-.wy-table-responsive {
-  overflow: visible !important;
+  .wy-table-responsive {
+    overflow: visible !important;
+  }
 }
+
+/* Small easter-egg logo sizing */
+.wy-side-nav-search .logo img,
+.wy-side-nav .logo img,
+.rst-sidebar .logo img,
+.logo img {
+  max-width: 80px;
+  margin: 6px 8px;
+  height: auto;
 }

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/api/decks.rst

@@ -25,7 +25,7 @@ InputDeckIO
 
    .. code-block:: python
 
-       from osiris_utils.decks import InputDeckIO
+       from osiris_utils import InputDeckIO
 
        # Load an input deck
        deck = InputDeckIO("osiris.inp")

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/api/postprocess.rst

@@ -86,7 +86,7 @@ Derivative_Simulation Class
        from osiris_utils.postprocessing import Derivative_Simulation
        
        # Create a simulation interface
-       sim = Simulation('/path/to/input/deck')
+       sim = Simulation('/path/to/input/deck.inp')
        
        # Create a derivative processor for x₁ derivatives
        dx1 = Derivative_Simulation(sim, 'x1')
@@ -206,7 +206,7 @@ This example shows how to compute the z-component of curl(B):
     from osiris_utils.postprocessing import Derivative
     
     # Setup
-    sim = Simulation('/path/to/input/deck')
+    sim = Simulation('/path/to/input/deck.inp')
     dx1 = Derivative_Simulation(sim, 'x1')
     dx2 = Derivative_Simulation(sim, 'x2')
 
@@ -227,7 +227,7 @@ This example shows how to compute the divergence of E:
     from osiris_utils.postprocessing import Derivative_Diagnostic
     
     # Setup
-    e1 = Diagnostic('/path/to/folder', Species, "path/to/input/deck")
+    e1 = Diagnostic('/path/to/folder', species=None, input_deck="/path/to/input/deck.inp")
     
     # Create derivative processor for x₁ and x₂ derivatives
     de1_dx1 = Derivative_Diagnostic(e1, 'x1')
@@ -281,7 +281,7 @@ FFT_Simulation Class
        from osiris_utils.postprocessing import FFT_Simulation
        
        # Create a simulation interface
-       sim = Simulation('/path/to/input/deck')
+       sim = Simulation('/path/to/input/deck.inp')
        
        # Create an FFT processor for the first spatial dimension
        fft = FFT_Simulation(sim, 1)
@@ -379,7 +379,7 @@ This example shows how to compute and visualize a dispersion relation:
     import matplotlib.pyplot as plt
     
     # Setup
-    sim = Simulation('/path/to/input/deck')
+    sim = Simulation('/path/to/input/deck.inp')
     
     # Create FFT processor for both time and space
     # We'll do a 2D FFT - time (axis 0) and x1 (axis 1)
@@ -467,7 +467,7 @@ MFT_Simulation Class
        from osiris_utils.postprocessing import MFT_Simulation
        
        # Create a simulation interface
-       sim = Simulation('/path/to/input/deck')
+       sim = Simulation('/path/to/input/deck.inp')
        
        # Create MFT analyzer for x₁ direction (axis=1)
        mft = MFT_Simulation(sim, 1)
@@ -643,7 +643,7 @@ FieldCentering_Simulation Class
        from osiris_utils.postprocessing import FieldCentering_Simulation
 
        # Create a simulation interface
-       sim = Simulation('/path/to/input/deck')
+       sim = Simulation('/path/to/input/deck.inp')
 
        # Create a field centering processor
        centered_sim = FieldCentering_Simulation(sim)

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/api/sim_diag.rst

@@ -36,8 +36,8 @@ Simulation Class
    
        from osiris_utils.data import Simulation
        
-       # Create a simulation interface for electron data
-       sim = Simulation('path/to/simulation', "name_of_input_deck")
+       # Create a simulation interface
+       sim = Simulation('path/to/simulation/osiris.inp')
        
        # Access the E1 field diagnostic (doesn't load data yet) - this is a Diagnostic object
        # Since it is a diagnostic not related with the species, the species argument is not needed
@@ -63,7 +63,7 @@ Simulation Class
        b3 = sim['b3']
        
        # Load specific timesteps
-       e1[10:20]  # Load timesteps 10-19
+       e1[10:20, 0:10]  # Load timesteps 10-19 and x1 0-10
        
        # Clean up to free memory
        sim.delete_diagnostic('e1')
@@ -134,7 +134,9 @@ Diagnostic Base Class
    .. code-block:: python
    
        # Create diagnostic for electron charge
-       diag = Diagnostic("/path/to/simulation", species)
+       # Note: Use Simulation class for easier access instead of Diagnostic directly
+       electrons = Species("electrons", rqm=-1, q=-1)
+       diag = Diagnostic("/path/to/simulation", species=electrons)
        diag.get_quantity("charge")
        
        # Access specific timestep (without loading all data)
@@ -151,7 +153,7 @@ Diagnostic Base Class
    .. code-block:: python
    
        # Operations between diagnostics
-       sim = Simulation("/path/to/simulation", species)
+       sim = Simulation("/path/to/simulation/osiris.inp")
        e1 = sim["e1"]
        vfl1 = sim["electron"]["vfl1"]
        
@@ -221,7 +223,7 @@ One of the most powerful features of the Diagnostic system is that new diagnosti
 .. code-block:: python
 
     # Create base diagnostics
-    sim = Simulation("/path/to/simulation", "file_input_deck")
+    sim = Simulation("/path/to/simulation/osiris.inp")
     e1 = sim["e1"]
     e2 = sim["e2"] 
     e3 = sim["e3"]

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/api/utilities.rst

@@ -79,7 +79,7 @@ Particle Data
    .. code-block:: python
   
       import osiris_utils as ou  
-      raw = ou.raw = ou.OsirisRawFile("path/to/raw/file.h5")
+      raw = ou.OsirisRawFile("path/to/raw/file.h5")
       print(raw.data.keys())
       print(raw.data["x1"][0:10])  # Access x1 position of first 10 particles
 
@@ -107,7 +107,7 @@ Particle Data
          raw = ou.OsirisRawFile("path/to/raw/file/.../.h5")
          # Selecting 5 random tags from particles with energy>5
          mask = raw.data["ene"] >    5.
-         raw_to_file_tags("output.tag", type="random", n_tags=5, mask=mask)
+         raw.raw_to_file_tags("output.tag", type="random", n_tags=5, mask=mask)
 
 
 
@@ -149,7 +149,7 @@ TRACK Data
    .. code-block:: python
   
       import osiris_utils as ou
-      track = ou.OsirisTrackFile(path/to/track_file.h5)
+      track = ou.OsirisTrackFile("path/to/track_file.h5")
       print(track.data[0:10, :]["x1"]) # Access x1 position of first 10 particles over all time steps
 
 
@@ -175,7 +175,7 @@ Convert track file to the older more readable format
    .. code-block:: python
       
       >>> import osiris_utils as ou 
-      >>> ou.utils.convert_tracks('path/to/input_trackfile.h5')
+      >>> ou.convert_tracks('path/to/input_trackfile.h5')
       >>> # The output will be saved as 'path/to/input_trackfile-v2.h5'
 
    **Notes:**  
@@ -209,7 +209,7 @@ To create a tag file directly from raw data, see :class:`osiris_utils.data.data.
       import osiris_utils as ou 
       import numpy as np
       tags = np.array([[1, 12345], [2, 67890], [3, 11111]])  # Example tags
-      ou.utils.create_file_tags('output.tag', tags)
+      ou.create_file_tags('output.tag', tags)
       # This will generate a file 'output.tag' with the particle tags.
 
    **Notes:**  

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/conf.py

@@ -52,11 +52,30 @@ extensions = [
 nb_execution_mode = "off"  # use stored output; avoids long CI builds
 # options for sphinx_github_style
 top_level = "OSIRIS Utils"
-linkcode_blob = "head"
+linkcode_blob = "main"
 linkcode_url = r"https://github.com/joaopedrobiu6/osiris_utils/"
 linkcode_link_text = "Source"
 
 
+def linkcode_resolve(domain, info):
+    """Return a URL to the source code for ``info``.
+
+    This implementation avoids invoking git or requiring a tag; it
+    constructs URLs pointing at the `linkcode_blob` branch on GitHub.
+    """
+    if domain != "py":
+        return None
+
+    module = info.get("module")
+    if not module:
+        return None
+
+    # Convert module path to file path
+    filename = module.replace(".", "/") + ".py"
+
+    return f"{linkcode_url}blob/{linkcode_blob}/{filename}"
+
+
 # numpydoc_class_members_toctree = False
 # Napoleon settings
 napoleon_google_docstring = False
@@ -81,11 +100,11 @@ templates_path = ["_templates"]
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-source_suffix = [".rst", ".md"]
-# source_suffix = {
-#     '.rst': 'restructuredtext',
-#     '.md': 'markdown',
-# }
+# source_suffix = [".rst", ".md"]
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
 # The master toctree document.
 master_doc = "index"
 
@@ -136,7 +155,7 @@ html_css_files = ["custom.css"]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-# html_logo = '_static/images/logo_small_clear.png'
+html_logo = '_static/Imagem1.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/examples/example_InputDeck.md

@@ -93,7 +93,7 @@ print('After', deck['simulation'])
 ```python
 # add a parameter
 print("Before", deck["simulation"])
-deck.set_param("simulation", "new_parameter", value='HI!', unexistent_ok=True)
+deck.set_param("simulation", "new_parameter", value='HI', unexistent_ok=True)
 print("After", deck["simulation"])
 ```
 
@@ -144,5 +144,6 @@ Once you did your changes, you can simply generate a new input deck with `print_
 
 ```python
 deck.print_to_file("edited-deck.1d")
-! cat edited-deck.1d
+with open("edited-deck.1d") as f:
+    print(f.read())
 ```

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/docs/source/examples/example_Simulation_Diagnostic.md

@@ -13,14 +13,14 @@ import osiris_utils as ou
 
 # Example notebook for the `Simulation` and `Diagnostic` classes
 
-### `Simulation`
+## `Simulation`
 The `Simulation` class takes in:
 - `simulation_folder`: the folder where the input deck is located
 - `species`: the species in case we are interested in diagnostics that are species-specific (such as vfl1, T11, etc.)
 
 Acts as a wrapper for the `Diagnostic` class, allowing for an easy access to diagnostics of the simulation using a **dictionary-like** syntax.
 
-### `Diagnostic`
+## `Diagnostic`
 
 The `Diagnostic` class takes in:
 - `simulation_folder`: the folder where the input deck is located
@@ -46,7 +46,7 @@ print(sim.__dict__.keys())
 print(f"\n")
 
 # e3 is a Diagnostic object
-e3 = ou.Diagnostic("example_data", "electrons")
+e3 = ou.Diagnostic(simulation_folder="example_data")
 # now we need to load the data
 e3.get_quantity("e3")  # it knows the path there since OSIRIS always saves the data in the same way
 

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/osiris_utils/data/data.py

@@ -186,7 +186,7 @@ class OsirisGridFile(OsirisData):
         Field label/name (LaTeX formatted, e.g., r'$E_x$')
     """
 
-    def __init__(self, filename, data_slice: slice | None = None):
+    def __init__(self, filename, data_slice: slice | None = None, load_data: bool = True):
         super().__init__(filename)
 
         variable_key = self._get_variable_key(self._file)
@@ -195,12 +195,14 @@ class OsirisGridFile(OsirisData):
         self._label = self._file.attrs["LABEL"][0].decode("utf-8")
         self._FFTdata = None
 
-        data = np.array(self._file[variable_key][:]) if data_slice is None else np.array(self._file[variable_key][data_slice])
+        # Use dataset.shape to obtain sizes without loading full data when possible
+        dset = self._file[variable_key]
 
         axis = list(self._file["AXIS"].keys())
         if len(axis) == 1:
             self._grid = self._file["AXIS/" + axis[0]][()]
-            self._nx = len(data)
+            # nx for 1D is dataset length along its only axis
+            self._nx = dset.shape[0]
             self._dx = (self.grid[1] - self.grid[0]) / self.nx
             self._x = np.arange(self.grid[0], self.grid[1], self.dx)
         else:
@@ -208,15 +210,14 @@ class OsirisGridFile(OsirisData):
             for ax in axis:
                 grid.append(self._file["AXIS/" + ax][()])
             self._grid = np.array(grid)
-            self._nx = self._file[variable_key][()].transpose().shape
+            # use dataset.shape to avoid reading the whole dataset
+            # dataset stored may need transpose to match expected ordering; preserve shape only
+            self._nx = tuple(dset.shape[::-1]) if len(dset.shape) > 1 else (dset.shape[0],)
             self._dx = (self.grid[:, 1] - self.grid[:, 0]) / self.nx
 
-            # There's an issue when the dimension is 3 and we want to plot a 2D phasespace. I believe this
-            # is a problem for all cases where the dim != dim_of_phasespace
             try:
                 self._x = [np.arange(self.grid[i, 0], self.grid[i, 1], self.dx[i]) for i in range(self.dim)]
-            except Exception as e:
-                print(f"Error occurred while creating spatial coordinates: {e}")
+            except Exception:
                 self._x = [np.arange(self.grid[i, 0], self.grid[i, 1], self.dx[i]) for i in range(1)]
 
         self._axis = []
@@ -231,7 +232,13 @@ class OsirisGridFile(OsirisData):
             }
             self._axis.append(axis_data)
 
-        self._data = np.ascontiguousarray(data.T)
+        # Only load data if explicitly requested. Otherwise keep a placeholder so metadata-only
+        # initializations are cheap for large files.
+        if load_data:
+            data = np.array(dset[:]) if data_slice is None else np.array(dset[data_slice])
+            self._data = np.ascontiguousarray(data.T)
+        else:
+            self._data = None
 
         self._close_file()
 

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/osiris_utils/data/diagnostic.py

@@ -398,7 +398,7 @@ class Diagnostic:
             for file_num in range(1, self._maxiter + 1):
                 path_file = os.path.join(file_template + f"{file_num:06d}.h5")
                 if os.path.exists(path_file):
-                    dump = OsirisGridFile(path_file)
+                    dump = OsirisGridFile(path_file, load_data=False)
                     self._dx = dump.dx
                     self._nx = dump.nx
                     self._x = dump.x

{osiris_utils-1.2.0 → osiris_utils-1.2.2/osiris_utils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.2.0
+Version: 1.2.2
 Summary: Utilities to manipulate and visualise OSIRIS plasma PIC output data
 Author-email: João Pedro Ferreira Biu <joaopedrofbiu@tecnico.ulisboa.pt>
 License: MIT
@@ -43,6 +43,11 @@ Dynamic: license-file
 
 OSIRIS_UTILS
 ============
+.. image:: https://raw.githubusercontent.com/joaopedrobiu6/osiris_utils/main/docs/source/_static/Imagem1.png
+   :width: 200px
+   :align: right
+
+
 |Pypi|
 
 .. image:: https://github.com/joaopedrobiu6/osiris_utils/actions/workflows/ci.yml/badge.svg
@@ -158,3 +163,4 @@ Contributors
 - Diogo Carvalho
 - João Cândido
 - Margarida Pereira
+

{osiris_utils-1.2.0 → osiris_utils-1.2.2}/osiris_utils.egg-info/SOURCES.txt

@@ -18,6 +18,7 @@ docs/source/conf.py
 docs/source/contrib.rst
 docs/source/examples.rst
 docs/source/index.rst
+docs/source/_static/Imagem1.png
 docs/source/_static/custom.css
 docs/source/_static/quick_start_ez.png
 docs/source/api/decks.rst