PyCosmoMMF 0.0.6__tar.gz → 0.0.8__tar.gz

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyCosmoMMF
-Version: 0.0.6
+Version: 0.0.8
 Summary: A package for detecting structures in the Cosmic Web.
 Home-page: https://github.com/James11222/PyCosmoMMF/
 Author: James Sunseri

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/PyCosmoMMF/__init__.py

@@ -10,7 +10,14 @@ import pkg_resources
 
 test_field = np.load(pkg_resources.resource_filename(__name__, 'test_density_cube.npy'))
 
-__version__ = '0.0.5'
+def version():
+    """
+    Print the version of the package.
+    """
+    __version__ = '0.0.8'
+
+    print("PyCosmoMMF version: ", __version__)
+
 
 
 

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/PyCosmoMMF/filter.py

@@ -26,9 +26,9 @@ def wavevectors3D(dims, box_size=(2*np.pi, 2*np.pi, 2*np.pi)):
         The wavevectors in each dimension.
     """
     sample_rate = 2*np.pi * (np.array(dims) / box_size)
-    kx = np.fft.fftfreq(dims[0], 1/sample_rate[0]) * (2*np.pi / dims[0])
-    ky = np.fft.fftfreq(dims[1], 1/sample_rate[1]) * (2*np.pi / dims[1])
-    kz = np.fft.fftfreq(dims[2], 1/sample_rate[2]) * (2*np.pi / dims[2])
+    kx = (np.fft.fftfreq(dims[0], 1/sample_rate[0]) * (2*np.pi / dims[0])).astype(np.float32)
+    ky = (np.fft.fftfreq(dims[1], 1/sample_rate[1]) * (2*np.pi / dims[1])).astype(np.float32)
+    kz = (np.fft.fftfreq(dims[2], 1/sample_rate[2]) * (2*np.pi / dims[2])).astype(np.float32)
     return kx, ky, kz
 
 @jit_compiler
@@ -50,7 +50,7 @@ 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))
+    filter_k = np.zeros((nx, ny, nz), dtype=np.float32)
     for ix in nb.prange(nx):
         for iy in range(ny):
             for iz in range(nz):
@@ -78,7 +78,7 @@ def kspace_top_hat_filter(R_S, kv):
 
     kx, ky, kz = kv
     nx, ny, nz = len(kx), len(ky), len(kz)
-    filter_k = np.zeros((nx, ny, nz))
+    filter_k = np.zeros((nx, ny, nz), dtype=np.float32)
 
     for ix in nb.prange(nx):
         for iy in range(ny):
@@ -112,7 +112,7 @@ def smooth_top_hat(f, R_S, kv):
     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
+    return f_Rn.astype(np.float32)
 
 def smooth_gauss(f, R_S, kv):
     """
@@ -135,7 +135,7 @@ def smooth_gauss(f, R_S, kv):
     GF = kspace_gaussian_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
+    return f_Rn.astype(np.float32)
 
 
 def smooth_loggauss(f, R_S, kv):
@@ -178,5 +178,5 @@ def smooth_loggauss(f, R_S, kv):
     norm = np.sum(f) / np.sum(f_result)
     f_result *= norm
 
-    return f_result
+    return f_result.astype(np.float32)
 

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/PyCosmoMMF/hessian.py

@@ -30,7 +30,7 @@ def fast_hessian_from_smoothed(f_Rn, R_S, kv):
 
     f_Rn_hat = np.fft.fftn(f_Rn)
     dims = f_Rn_hat.shape
-    hessian = np.zeros((dims[0], dims[1], dims[2], 6), dtype=np.complex128)
+    hessian = np.zeros((dims[0], dims[1], dims[2], 6), dtype=np.complex64)
     kx, ky, kz = kv[0], kv[1], kv[2]
 
     @jit_compiler

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/PyCosmoMMF/signatures.py

@@ -29,7 +29,7 @@ def signatures_from_hessian(hessian):
     """
     
     hsize = hessian.shape[:3]
-    sigs = np.zeros((hsize[0], hsize[1], hsize[2], 3))
+    sigs = np.zeros((hsize[0], hsize[1], hsize[2], 3), dtype=np.float32)
 
     #helper functions
     def θ(x):
@@ -59,20 +59,25 @@ def signatures_from_hessian(hessian):
                 ])
                 
                 e1, e2, e3 = np.sort(np.real(np.linalg.eigvals(hes_slice)))
-            
-                sigs[i,j,k,0] = (np.abs(e3 / e1) *
-                    np.abs(e3)) * (θ(-e1) * θ(-e2) * θ(-e3))
-                
-                sigs[i,j,k,1] = (np.abs(e2 / e1) *
-                    xθ(1-np.abs(e3 / e1))) * (np.abs(e2) * θ(-e1) * θ(-e2) )
-                
-                sigs[i,j,k,2] = (xθ(1-np.abs(e2 / e1)) *
-                    xθ(1-np.abs(e3 / e1))) * (np.abs(e1) * θ(-e1))
+
+                if e1 == 0:
+                    sigs[i,j,k,0] = 0
+                    sigs[i,j,k,1] = 0
+                    sigs[i,j,k,2] = 0
+                else:
+                    sigs[i,j,k,0] = (np.abs(e3 / e1) *
+                        np.abs(e3)) * (θ(-e1) * θ(-e2) * θ(-e3))
+                    
+                    sigs[i,j,k,1] = (np.abs(e2 / e1) *
+                        xθ(1-np.abs(e3 / e1))) * (np.abs(e2) * θ(-e1) * θ(-e2) )
+                    
+                    sigs[i,j,k,2] = (xθ(1-np.abs(e2 / e1)) *
+                        xθ(1-np.abs(e3 / e1))) * (np.abs(e1) * θ(-e1))
     
     return sigs
 
 
-def maximum_signature(Rs, field, alg='NEXUSPLUS'):
+def maximum_signature(Rs, field, alg='NEXUSPLUS', eps=1e-8):
     """
     Compute the maximum signatures across all scales Rs.
 
@@ -85,6 +90,8 @@ def maximum_signature(Rs, field, alg='NEXUSPLUS'):
     alg : string, optional
         The algorithm to use. Can be either 'NEXUS' or 'NEXUSPLUS'.
         Default is 'NEXUSPLUS'.
+    eps : float, optional
+        A small number to avoid division by zero errors and whatnot. Default is 1e-8.
 
     Returns
     -------
@@ -97,13 +104,13 @@ def maximum_signature(Rs, field, alg='NEXUSPLUS'):
     nx, ny, nz = field.shape
     
     # Make sure the field has no 0 values
-    field = field + 0.0001
+    field = field + eps
     
     # Calculate wave vectors for our field
     wave_vecs = wavevectors3D((nx, ny, nz))
     
     # Calculate signatures at each scale Rn, determine max
-    sigmax = np.ones((nx, ny, nz, 3)) * 0.00001
+    sigmax = np.ones((nx, ny, nz, 3), dtype=np.float32) * eps
 
     @jit_compiler
     def perform_loop(sigmax, sigs_Rn, nx, ny, nz):

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/PyCosmoMMF.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyCosmoMMF
-Version: 0.0.6
+Version: 0.0.8
 Summary: A package for detecting structures in the Cosmic Web.
 Home-page: https://github.com/James11222/PyCosmoMMF/
 Author: James Sunseri

{PyCosmoMMF-0.0.6 → PyCosmoMMF-0.0.8}/setup.py

@@ -12,7 +12,7 @@ here = pathlib.Path(__file__).parent.resolve()
 
 setup(
     name='PyCosmoMMF',  # Required
-    version='0.0.6',  # Required
+    version='0.0.8',  # 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)