PyCosmoMMF 0.2.0__tar.gz → 0.4.0__tar.gz

{pycosmommf-0.2.0 → pycosmommf-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pycosmommf
-Version: 0.2.0
+Version: 0.4.0
 Summary: A package for identifying structures in the cosmic web.
 Project-URL: Homepage, https://github.com/James11222/pycosmommf
 Project-URL: Bug Tracker, https://github.com/James11222/pycosmommf/issues

{pycosmommf-0.2.0 → pycosmommf-0.4.0}/src/pycosmommf/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.4.0'
+__version_tuple__ = version_tuple = (0, 4, 0)

{pycosmommf-0.2.0 → pycosmommf-0.4.0}/src/pycosmommf/tagging.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 
-import functools
-
+import numba as nb
 import numpy as np
 import skimage.measure
 
+jit_compiler = nb.njit(parallel=True, fastmath=True)
+
 
 def make_the_clusbool(delta, max_sigs, Δ):  # pragma: no cover
     """
@@ -16,43 +17,57 @@ def make_the_clusbool(delta, max_sigs, Δ):  # pragma: no cover
     change in virialization fraction as a function of 𝒮_cluster.
 
     Arguments:
-
+    ----------------
     delta - [3D Float Array] - delta refers to the δ delta.
     max_sigs - [4D Float Array] - the maximum signatures array from CosmoMMF.maximum_signature()
     verbose - [Boolean] - a flag to allow the function to be more helpful and verbose.
     Δ - [Int] - The overdensity parameter threshold for determining virialization. This
     parameter comes from a paper by Gunn & Gott on spherical collapse. Commonly
     used values that are physically motivated can be 370, 200, or 500 (for R_200 or R_500).
+
+    Returns:
+    ----------------
+    clusbool - [3D Boolean Array] - a boolean filter that selects only the clusters in a given cosmological δ field.
+    S_th - [Float] - the threshold value for 𝒮_cluster.
+    signature_thresholds - [1D Float Array] - an array of threshold values for 𝒮_cluster.
+    virialized_fractions - [1D Float Array] - an array of virialized fractions as a function of 𝒮_cluster.
     """
 
     signature_thresholds = np.geomspace(0.1, 30, 10)  # hard coded for now
     virialized_fractions = np.zeros_like(signature_thresholds)
 
-    def check_virialized(j, delta, clumps, Δ):
-        δ_ave = np.mean(delta[clumps == j])
-        return int(δ_ave > Δ)
+    @jit_compiler
+    def calc_virialized_fraction(clumps):
+        nx, ny, nz = clumps.shape
+
+        total_clumps_detected = np.max(clumps)
+        summed_overdensity_per_clump = np.zeros(total_clumps_detected)
+        num_cells_per_clump = np.zeros(total_clumps_detected)
+
+        for i in nb.prange(nx):
+            for j in range(ny):
+                for k in range(nz):
+                    if clumps[i, j, k] != 0:
+                        clump_id = int(
+                            clumps[i, j, k]
+                        )  # clump_id is the clump number ranging from 1 to total_clumps_detected
+                        summed_overdensity_per_clump[clump_id - 1] += delta[i, j, k]
+                        num_cells_per_clump[clump_id - 1] += 1
+
+        return summed_overdensity_per_clump / num_cells_per_clump
 
     for i, S_th in enumerate(signature_thresholds):
         # Identify Clumps with S > S_th
         _clusbool = max_sigs[:, :, :, 0] > S_th
+
         clumps = skimage.measure.label(
-            _clusbool
+            _clusbool.astype(int)
         )  # an array where 0 is background and 1, 2, 3, ... are the clumps
-        total_clumps_detected = np.max(clumps)
+        averaged_overdensity_per_clump = calc_virialized_fraction(clumps)
 
-        num_clumps_virialized = np.sum(
-            list(
-                map(
-                    functools.partial(
-                        check_virialized, delta=delta, clumps=clumps, Δ=Δ
-                    ),
-                    range(1, total_clumps_detected + 1),
-                )
-            )
-        )  # number of clumps that are virialized
-
-        # Calculate the number of virialized clumps
-        virialized_fractions[i] = num_clumps_virialized / total_clumps_detected
+        virialized_fractions[i] = np.sum(averaged_overdensity_per_clump > Δ) / np.max(
+            clumps
+        )
 
     S_th = signature_thresholds[np.abs(virialized_fractions - 0.5).argmin()]
     clusbool = max_sigs[:, :, :, 0] > S_th

pycosmommf-0.2.0/serve/.buildinfo

@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 71380b8691105fdaf5c9bc417d4961a1
-tags: 645f666f9bcd5a90fca523b33c5a78b7

pycosmommf-0.2.0/serve/.buildinfo.bak

@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: d92f197c1635a88a2c9a049b675e43a8
-tags: 645f666f9bcd5a90fca523b33c5a78b7

pycosmommf-0.2.0/serve/API.html

@@ -1,506 +0,0 @@
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-    <link rel="search" title="Search" href="search.html" />
-
-    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
-    <title>
-      API Docs - pycosmommf 0.1.3.dev4+gd17e420.d20241114 documentation
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-                  ><svg><use href="#svg-toc"></use></svg
-                ></i>
-              </label>
-            </div>
-            <article role="main" id="furo-main-content">
-              <section id="api-docs">
-                <h1>
-                  API Docs<a
-                    class="headerlink"
-                    href="#api-docs"
-                    title="Link to this heading"
-                    >¶</a
-                  >
-                </h1>
-                <ul class="simple">
-                  <li>
-                    <p>
-                      <a class="reference internal" href="genindex.html"
-                        ><span class="std std-ref">Index</span></a
-                      >
-                    </p>
-                  </li>
-                  <li>
-                    <p>
-                      <a class="reference internal" href="py-modindex.html"
-                        ><span class="std std-ref">Module Index</span></a
-                      >
-                    </p>
-                  </li>
-                  <li>
-                    <p>
-                      <a class="reference internal" href="search.html"
-                        ><span class="std std-ref">Search Page</span></a
-                      >
-                    </p>
-                  </li>
-                </ul>
-              </section>
-            </article>
-          </div>
-          <footer>
-            <div class="related-pages"></div>
-            <div class="bottom-of-page">
-              <div class="left-details">
-                <div class="copyright">
-                  Copyright &#169; 2024, James Sunseri
-                </div>
-                Made with <a href="https://www.sphinx-doc.org/">Sphinx</a> and
-                <a class="muted-link" href="https://pradyunsg.me">@pradyunsg</a
-                >'s
-
-                <a href="https://github.com/pradyunsg/furo">Furo</a>
-              </div>
-              <div class="right-details"></div>
-            </div>
-          </footer>
-        </div>
-        <aside class="toc-drawer no-toc"></aside>
-      </div>
-    </div>
-    <script src="_static/documentation_options.js?v=27e77f62"></script>
-    <script src="_static/doctools.js?v=9bcbadda"></script>
-    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-    <script src="_static/scripts/furo.js?v=5fa4622c"></script>
-    <script src="_static/clipboard.min.js?v=a7894cd8"></script>
-    <script src="_static/copybutton.js?v=f281be69"></script>
-  </body>
-</html>

pycosmommf-0.2.0/serve/_sources/API.md.txt

@@ -1,10 +0,0 @@
-```{include} ../README.md
-:start-after: <!-- start elevator-pitch -->
-:end-before: <!-- end elevator-pitch -->
-```
-
-## API Docs
-
-- {ref}`genindex`
-- {ref}`modindex`
-- {ref}`search`