PyCosmoMMF 0.0.4__tar.gz → 0.0.5__tar.gz

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyCosmoMMF
-Version: 0.0.4
+Version: 0.0.5
 Summary: A package for detecting structures in the Cosmic Web.
 Home-page: https://github.com/James11222/PyCosmoMMF/
 Author: James Sunseri

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF/__init__.py

@@ -6,10 +6,14 @@ from PyCosmoMMF.hessian import *
 from PyCosmoMMF.tagging import *
 from PyCosmoMMF.utils import *
 from PyCosmoMMF.signatures import *
-
-
 import pkg_resources
+
 test_field = np.load(pkg_resources.resource_filename(__name__, 'test_density_cube.npy'))
 
+__version__ = '0.0.5'
+
+
+
+
 
 

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF/filter.py

@@ -1,5 +1,13 @@
 import numpy as np
 import numba as nb
+from PyCosmoMMF.utils import *
+
+# if parallel_flag == True:
+#     jit_compiler = nb.njit(parallel=True, fastmath=True)
+# else:
+#     jit_compiler = nb.njit(fastmath=True)
+
+jit_compiler = nb.njit(fastmath=True)
 
 def wavevectors3D(dims, box_size=(2*np.pi, 2*np.pi, 2*np.pi)):
     """
@@ -23,7 +31,7 @@ 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
 
-@nb.njit(parallel=True, fastmath=True)
+@jit_compiler
 def kspace_gaussian_filter(R_S, kv):
     """
     create a Gaussian filter in k-space.
@@ -50,7 +58,7 @@ def kspace_gaussian_filter(R_S, kv):
                     -(kx[ix]**2 + ky[iy]**2 + kz[iz]**2) * R_S**2 / 2)
     return filter_k
 
-@nb.njit(parallel=True, fastmath=True)
+@jit_compiler
 def kspace_top_hat_filter(R_S, kv):
     """
     create a top-hat filter in k-space.

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF/hessian.py

@@ -1,5 +1,13 @@
 import numpy as np
 import numba as nb
+from PyCosmoMMF.utils import *
+
+# if parallel_flag == True:
+#     jit_compiler = nb.njit(parallel=True, fastmath=True)
+# else:
+#     jit_compiler = nb.njit(fastmath=True)
+
+jit_compiler = nb.njit(fastmath=True)
 
 def fast_hessian_from_smoothed(f_Rn, R_S, kv):
     """
@@ -25,7 +33,7 @@ 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]
 
-    @nb.njit(parallel=True, fastmath=True)
+    @jit_compiler
     def perform_loop(hessian):
         """
         This function is a loop that calculates the hessian matrix

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF/signatures.py

@@ -3,8 +3,16 @@ import numba as nb
 
 from PyCosmoMMF.filter import *
 from PyCosmoMMF.hessian import *
+from PyCosmoMMF.utils import *
 
-@nb.njit(parallel=True)
+# if parallel_flag == True:
+#     jit_compiler = nb.njit(parallel=True)
+# else:
+#     jit_compiler = nb.njit
+
+jit_compiler = nb.njit
+
+@jit_compiler
 def signatures_from_hessian(hessian):
     """
     Function to calculate the signatures from a given hessian.
@@ -97,7 +105,7 @@ def maximum_signature(Rs, field, alg='NEXUSPLUS'):
     # Calculate signatures at each scale Rn, determine max
     sigmax = np.ones((nx, ny, nz, 3)) * 0.00001
 
-    @nb.njit(parallel=True)
+    @jit_compiler
     def perform_loop(sigmax, sigs_Rn, nx, ny, nz):
         for ix in nb.prange(nx):
             for iy in range(ny):

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF/tagging.py

@@ -3,7 +3,14 @@ import numpy as np
 import matplotlib.pyplot as plt
 from skimage.measure import label
 import numba as nb
+from PyCosmoMMF.utils import *
 
+# if parallel_flag == True:
+#     jit_compiler = nb.njit(parallel=True, fastmath=True)
+# else:
+#     jit_compiler = nb.njit(fastmath=True)
+
+jit_compiler = nb.njit(fastmath=True)
 
 def make_the_clusbool(data, max_sigs, verbose, Δ):
     """
@@ -68,7 +75,7 @@ def make_the_clusbool(data, max_sigs, verbose, Δ):
     volume = np.zeros(total_clusters_detected + 1)
     signatures = np.zeros(total_clusters_detected + 1)
 
-    @nb.njit(parallel=True, fastmath=True)
+    @jit_compiler
     def perform_loop(density, volume, signatures, data, max_sigs):
         for i in nb.prange(nx):
             for j in range(ny):

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF/utils.py

@@ -1,4 +1,8 @@
 import numpy as np
+import os
+
+#by default we set the parallel flag to False
+# parallel_flag = False
 
 def test_print():
     """
@@ -15,4 +19,4 @@ def shrink(data, new_size):
     zs = new_size
     return data.reshape(xs, data.shape[0]//xs, 
                         ys, data.shape[1]//ys, 
-                        zs, data.shape[2]//zs).sum(axis=1).sum(axis=2).sum(axis=3)
+                        zs, data.shape[2]//zs).sum(axis=1).sum(axis=2).sum(axis=3)

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/PyCosmoMMF.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyCosmoMMF
-Version: 0.0.4
+Version: 0.0.5
 Summary: A package for detecting structures in the Cosmic Web.
 Home-page: https://github.com/James11222/PyCosmoMMF/
 Author: James Sunseri

{PyCosmoMMF-0.0.4 → PyCosmoMMF-0.0.5}/setup.py

@@ -12,7 +12,7 @@ here = pathlib.Path(__file__).parent.resolve()
 
 setup(
     name='PyCosmoMMF',  # Required
-    version='0.0.4',  # Required
+    version='0.0.5',  # 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)