PyCosmoMMF 0.0.1__tar.gz → 0.0.3__tar.gz

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/MANIFEST.in

@@ -4,4 +4,3 @@ include *.md
 include PyCosmoMMF/*.py
 include PyCosmoMMF/*.npy
 include MANIFEST.in
-include *.pypirc

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyCosmoMMF
-Version: 0.0.1
+Version: 0.0.3
 Summary: A package for detecting structures in the Cosmic Web.
 Home-page: https://github.com/James11222/PyCosmoMMF/
 Author: James Sunseri

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PyCosmoMMF/__init__.py

@@ -1,5 +1,5 @@
 import numpy as np
-from numba import njit
+import numba as nb
 
 from PyCosmoMMF.filter import *
 from PyCosmoMMF.hessian import *  

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PyCosmoMMF/filter.py

@@ -1,5 +1,5 @@
 import numpy as np
-from numba import njit
+import numba as nb
 
 def wavevectors3D(dims, box_size=(2*np.pi, 2*np.pi, 2*np.pi)):
     """
@@ -23,7 +23,7 @@ def wavevectors3D(dims, box_size=(2*np.pi, 2*np.pi, 2*np.pi)):
     kz = np.fft.fftfreq(dims[2], 1/sample_rate[2]) * (2*np.pi / dims[2])
     return kx, ky, kz
 
-@njit
+@nb.njit(parallel=True, fastmath=True)
 def kspace_gaussian_filter(R_S, kv):
     """
     create a Gaussian filter in k-space.
@@ -43,13 +43,69 @@ def kspace_gaussian_filter(R_S, kv):
     kx, ky, kz = kv
     nx, ny, nz = len(kx), len(ky), len(kz)
     filter_k = np.zeros((nx, ny, nz))
-    for ix in range(nx):
+    for ix in nb.prange(nx):
         for iy in range(ny):
             for iz in range(nz):
                 filter_k[ix, iy, iz] = np.exp(
                     -(kx[ix]**2 + ky[iy]**2 + kz[iz]**2) * R_S**2 / 2)
     return filter_k
 
+@nb.njit(parallel=True, fastmath=True)
+def kspace_top_hat_filter(R_S, kv):
+    """
+    create a top-hat filter in k-space.
+
+    Parameters
+    ----------
+    R_S : float
+        The smoothing scale.
+    kv : tuple
+        The wavevectors in each dimension.
+    
+    Returns
+    -------
+    filter_k : array
+        The filter in k-space.
+    """
+
+    kmax = (2 * np.pi) / R_S
+
+    kx, ky, kz = kv
+    nx, ny, nz = len(kx), len(ky), len(kz)
+    filter_k = np.zeros((nx, ny, nz))
+
+    for ix in range(nx):
+        for iy in range(ny):
+            for iz in range(nz):
+                if (np.sqrt(kx[ix]**2 + ky[iy]**2 + kz[iz]**2)) < kmax:
+                    filter_k[ix, iy, iz] = 1
+
+    return filter_k
+
+
+def smooth_top_hat(f, R_S, kv):
+    """
+    apply a top-hat filter to a field f.
+
+    Parameters
+    ----------
+    f : array
+        The field to be smoothed.
+    R_S : float
+        The smoothing scale.
+    kv : tuple
+        The wavevectors in each dimension.
+
+    Returns
+    -------
+    f_Rn : array
+        The smoothed field.
+    """
+    GF = kspace_top_hat_filter(R_S, kv)
+    f_Rn = np.real(np.fft.ifftn(GF * np.fft.fftn(f)))
+    f_Rn = f_Rn * (np.sum(f) / np.sum(f_Rn))
+    return f_Rn
+
 def smooth_gauss(f, R_S, kv):
     """
     apply a Gaussian filter to a field f.

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PyCosmoMMF/hessian.py

@@ -1,5 +1,5 @@
 import numpy as np
-from numba import njit
+import numba as nb
 
 def fast_hessian_from_smoothed(f_Rn, R_S, kv):
     """
@@ -25,13 +25,13 @@ def fast_hessian_from_smoothed(f_Rn, R_S, kv):
     hessian = np.zeros((dims[0], dims[1], dims[2], 6), dtype=np.complex128)
     kx, ky, kz = kv[0], kv[1], kv[2]
 
-    @njit
+    @nb.njit(parallel=True, fastmath=True)
     def perform_loop(hessian):
         """
         This function is a loop that calculates the hessian matrix
         for each point in the 3D array.
         """
-        for x in range(len(kv[0])):
+        for x in nb.prange(len(kv[0])):
             for y in range(len(kv[1])):
                 for z in range(len(kv[2])):
                     # (1,1)

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PyCosmoMMF/signatures.py

@@ -1,10 +1,10 @@
 import numpy as np
-from numba import njit
+import numba as nb
 
 from PyCosmoMMF.filter import *
 from PyCosmoMMF.hessian import *
 
-@njit
+@nb.njit(parallel=True)
 def signatures_from_hessian(hessian):
     """
     Function to calculate the signatures from a given hessian.
@@ -41,7 +41,7 @@ def signatures_from_hessian(hessian):
         return 0
     
     
-    for i in range(hsize[0]):
+    for i in nb.prange(hsize[0]):
         for j in range(hsize[1]):
             for k in range(hsize[2]):
                 hes_slice = np.array([
@@ -97,9 +97,9 @@ def maximum_signature(Rs, field, alg='NEXUSPLUS'):
     # Calculate signatures at each scale Rn, determine max
     sigmax = np.ones((nx, ny, nz, 3)) * 0.00001
 
-    @njit
+    @nb.njit(parallel=True)
     def perform_loop(sigmax, sigs_Rn, nx, ny, nz):
-        for ix in range(nx):
+        for ix in nb.prange(nx):
             for iy in range(ny):
                 for iz in range(nz):
                     for sigtype in range(3):

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PyCosmoMMF/tagging.py

@@ -2,7 +2,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from skimage.measure import label
-from numba import njit
+import numba as nb
 
 
 def make_the_clusbool(data, max_sigs, verbose, Δ):
@@ -68,9 +68,9 @@ def make_the_clusbool(data, max_sigs, verbose, Δ):
     volume = np.zeros(total_clusters_detected + 1)
     signatures = np.zeros(total_clusters_detected + 1)
 
-    @njit
+    @nb.njit(parallel=True, fastmath=True)
     def perform_loop(density, volume, signatures, data, max_sigs):
-        for i in range(nx):
+        for i in nb.prange(nx):
             for j in range(ny):
                 for k in range(nz):
                     if components[i,j,k] != 0:

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/PyCosmoMMF.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyCosmoMMF
-Version: 0.0.1
+Version: 0.0.3
 Summary: A package for detecting structures in the Cosmic Web.
 Home-page: https://github.com/James11222/PyCosmoMMF/
 Author: James Sunseri

{PyCosmoMMF-0.0.1 → PyCosmoMMF-0.0.3}/setup.py

@@ -12,7 +12,7 @@ here = pathlib.Path(__file__).parent.resolve()
 
 setup(
     name='PyCosmoMMF',  # Required
-    version='0.0.1',  # Required
+    version='0.0.3',  # Required
     description='A package for detecting structures in the Cosmic Web.',  # Optional
     long_description=(here / 'README.md').read_text(encoding='utf-8'),  # Optional
     long_description_content_type='text/markdown',  # Optional (see note above)
@@ -57,4 +57,4 @@ setup(
         'Check out my Website!': 'http://www.james-sunseri.com',
         'Source': 'https://github.com/James11222/PyCosmoMMF/',
     }
-)
+)