amaazetools 0.0.8__tar.gz → 0.1.0__tar.gz

{amaazetools-0.0.8/amaazetools.egg-info → amaazetools-0.1.0}/PKG-INFO

@@ -1,18 +1,26 @@
 Metadata-Version: 2.1
 Name: amaazetools
-Version: 0.0.8
+Version: 0.1.0
 Summary: Python package for mesh processing tools developed by AMAAZE
-Home-page: https://github.com/jwcalder/AMAAZETools
-Author: Jeff Calder
-Author-email: jwcalder@umn.edu
-License: UNKNOWN
-Platform: UNKNOWN
+Author-email: Jeff Calder <jwcalder@umn.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/jwcalder/AMAAZETools
+Project-URL: Bug Tracker, https://github.com/jwcalder/AMAAZETools/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: pydicom
+Requires-Dist: scikit-image
+Requires-Dist: sklearn
+Requires-Dist: matplotlib
+Requires-Dist: graphlearning
+Requires-Dist: plyfile
 
 # AMAAZE Tools
 
@@ -29,7 +37,7 @@ To install the most recent developers version of the package, run
 git clone https://github.com/jwcalder/AMAAZETools
 cd AMAAZETools
 pip install -r requirements.txt
-python setup.py install --user
+pip install .
 ```
 
 ## Documentation
@@ -47,5 +55,3 @@ Several people have contributed to the development of this software:
 1. David Floeder
 2. Riley O'Neill
 3. Brendan Cook
-
-

{amaazetools-0.0.8 → amaazetools-0.1.0}/README.md

@@ -13,7 +13,7 @@ To install the most recent developers version of the package, run
 git clone https://github.com/jwcalder/AMAAZETools
 cd AMAAZETools
 pip install -r requirements.txt
-python setup.py install --user
+pip install .
 ```
 
 ## Documentation

{amaazetools-0.0.8 → amaazetools-0.1.0}/amaazetools/trimesh.py

@@ -271,7 +271,7 @@ def synth_mesh(angle, num_pts):
     f = np.minimum(f,0.4 + z)
 
     #Marching cubes for isosurface
-    verts,faces,normals,values = measure.marching_cubes(f,0,spacing=(h,h,h))
+    verts,faces,normals,values = measure.marching_cubes(f,0,spacing=(h,h,h),allow_degenerate=False)
 
     #Adjust angle
     verts -= [1,1,1]
@@ -339,7 +339,7 @@ class mesh:
             The index of the given point as an integer.
         """
 
-        if type(point) in [np.int,np.int32,np.int64]:
+        if type(point) in [int,np.int32,np.int64]:
             point_ind=point
         elif type(point) == np.ndarray and len(point)==3:
             point_ind = np.argmin(np.linalg.norm(self.points - point,axis=1))
@@ -349,52 +349,6 @@ class mesh:
             sys.exit("'point' must be an integer index, or a length 3 list, tuple, or numpy ndarray (x,y,z)")
         return point_ind
 
-    def edge_points(self,u,k=7,return_mask=False,number=None):
-        """ Computes the edge points of the mesh.
-
-            Parameters
-            ----------
-            u : (num_verts,1) int array
-                Array of labels for each point.
-            k : int, default is 7
-                Number of nearest neighbors to use.
-            return_mask : boolean, default is False
-                If True, return edge_points as a (num,verts,) boolean array.
-            number : int, default is None
-                Max number of edge points to return.
-
-            Returns
-            -------
-            An int array containing the edge point indices.
-        """
-
-        W = gl.weightmatrix.knn(self.points,k,kernel='uniform',symmetrize=False)
-        d = gl.graph(W).degree_vector()
-        mask = d*u != W@u
-
-        #Select a few points spaced out along edge
-        if number is not None:
-            edge_ind = np.arange(self.num_verts())[mask]
-            edge_points = self.points[mask,:]
-            num_edge_points = len(edge_points)
-
-            #PCA
-            mean = np.mean(edge_points,axis=0)
-            cov = (edge_points-mean).T@(edge_points-mean)
-            l,v = sparse.linalg.eigs(cov,k=1,which='LM')
-            proj = (edge_points-mean)@v.real
-
-            #Sort along princpal axis
-            sort_ind = np.argsort(proj.flatten())
-            dx = (num_edge_points-1)/(number-1)
-            spaced_edge_ind = edge_ind[sort_ind[np.arange(0,num_edge_points,dx).astype(int)]]
-            mask = np.zeros(self.num_verts(),dtype=bool)
-            mask[spaced_edge_ind]=True
-
-        if return_mask:
-            return mask.astype(int)
-        else: #return indices
-            return np.arange(self.num_verts())[mask]
 
     def geodesic_patch(self,point,r,k=7,return_mask=False):
         """ Computes a geodesic patch around a specified point.
@@ -1052,7 +1006,7 @@ class mesh:
         euclidean_radius = np.max(np.linalg.norm(patch - center,axis=1))
 
         if return_edge_points:
-            E = self.edge_points(C_local,k=k,number=number_edge_points)
+            E = edge_points(patch,C_local,k=k,number=number_edge_points)
             E = patch_ind[E]
             if return_euclidean_radius:
                 return theta,n1,n2,C,E,euclidean_radius
@@ -1268,3 +1222,100 @@ def canonical_labels(u):
             u[J] = label
     return u
 
+def edge_points(points,u,k=7,return_mask=False,number=None):
+    """ Computes the edge points of the mesh.
+
+        Parameters
+        ----------
+        points : (n,3) float array
+            Coordinates of points.
+        u : (num_verts,1) int array
+            Array of labels for each point.
+        k : int, default is 7
+            Number of nearest neighbors to use.
+        return_mask : boolean, default is False
+            If True, return edge_points as a (num_verts,) boolean array.
+        number : int, default is None
+            Max number of edge points to return.
+
+        Returns
+        -------
+        An int array containing the edge point indices.
+    """
+
+    num_verts = points.shape[0]
+    W = gl.weightmatrix.knn(points,k,kernel='uniform',symmetrize=False)
+    d = gl.graph(W).degree_vector()
+    mask = d*u != W@u
+
+    #Select a few points spaced out along edge
+    if number is not None:
+        edge_ind = np.arange(num_verts)[mask]
+        edge_points = points[mask,:]
+        num_edge_points = len(edge_points)
+
+        #PCA
+        mean = np.mean(edge_points,axis=0)
+        cov = (edge_points-mean).T@(edge_points-mean)
+        l,v = sparse.linalg.eigs(cov,k=1,which='LM')
+        proj = (edge_points-mean)@v.real
+
+        #Sort along princpal axis
+        sort_ind = np.argsort(proj.flatten())
+        dx = (num_edge_points-1)/(number-1)
+        spaced_edge_ind = edge_ind[sort_ind[np.arange(0,num_edge_points,dx).astype(int)]]
+        mask = np.zeros(num_verts,dtype=bool)
+        mask[spaced_edge_ind]=True
+
+    if return_mask:
+        return mask.astype(int)
+    else: #return indices
+        return np.arange(num_verts)[mask]
+
+#def edge_points(self,u,k=7,return_mask=False,number=None):
+#    """ Computes the edge points of the mesh.
+#
+#        Parameters
+#        ----------
+#        u : (num_verts,1) int array
+#            Array of labels for each point.
+#        k : int, default is 7
+#            Number of nearest neighbors to use.
+#        return_mask : boolean, default is False
+#            If True, return edge_points as a (num,verts,) boolean array.
+#        number : int, default is None
+#            Max number of edge points to return.
+#
+#        Returns
+#        -------
+#        An int array containing the edge point indices.
+#    """
+#
+#    W = gl.weightmatrix.knn(self.points,k,kernel='uniform',symmetrize=False)
+#    d = gl.graph(W).degree_vector()
+#    mask = d*u != W@u
+#
+#    #Select a few points spaced out along edge
+#    if number is not None:
+#        edge_ind = np.arange(self.num_verts())[mask]
+#        edge_points = self.points[mask,:]
+#        num_edge_points = len(edge_points)
+#
+#        #PCA
+#        mean = np.mean(edge_points,axis=0)
+#        cov = (edge_points-mean).T@(edge_points-mean)
+#        l,v = sparse.linalg.eigs(cov,k=1,which='LM')
+#        proj = (edge_points-mean)@v.real
+#
+#        #Sort along princpal axis
+#        sort_ind = np.argsort(proj.flatten())
+#        dx = (num_edge_points-1)/(number-1)
+#        spaced_edge_ind = edge_ind[sort_ind[np.arange(0,num_edge_points,dx).astype(int)]]
+#        mask = np.zeros(self.num_verts(),dtype=bool)
+#        mask[spaced_edge_ind]=True
+#
+#    if return_mask:
+#        return mask.astype(int)
+#    else: #return indices
+#        return np.arange(self.num_verts())[mask]
+

{amaazetools-0.0.8 → amaazetools-0.1.0/amaazetools.egg-info}/PKG-INFO

@@ -1,18 +1,26 @@
 Metadata-Version: 2.1
 Name: amaazetools
-Version: 0.0.8
+Version: 0.1.0
 Summary: Python package for mesh processing tools developed by AMAAZE
-Home-page: https://github.com/jwcalder/AMAAZETools
-Author: Jeff Calder
-Author-email: jwcalder@umn.edu
-License: UNKNOWN
-Platform: UNKNOWN
+Author-email: Jeff Calder <jwcalder@umn.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/jwcalder/AMAAZETools
+Project-URL: Bug Tracker, https://github.com/jwcalder/AMAAZETools/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: pydicom
+Requires-Dist: scikit-image
+Requires-Dist: sklearn
+Requires-Dist: matplotlib
+Requires-Dist: graphlearning
+Requires-Dist: plyfile
 
 # AMAAZE Tools
 
@@ -29,7 +37,7 @@ To install the most recent developers version of the package, run
 git clone https://github.com/jwcalder/AMAAZETools
 cd AMAAZETools
 pip install -r requirements.txt
-python setup.py install --user
+pip install .
 ```
 
 ## Documentation
@@ -47,5 +55,3 @@ Several people have contributed to the development of this software:
 1. David Floeder
 2. Riley O'Neill
 3. Brendan Cook
-
-

{amaazetools-0.0.8 → amaazetools-0.1.0}/amaazetools.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 LICENSE
 MANIFEST.in
 README.md
+pyproject.toml
 setup.py
 amaazetools/__init__.py
 amaazetools/dicom.py

amaazetools-0.1.0/pyproject.toml

@@ -0,0 +1,38 @@
+[build-system]
+requires = ["setuptools","numpy"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.setuptools]
+packages = ['amaazetools']
+
+
+[project]
+name = "amaazetools"
+version = "0.1.0"
+authors = [
+  { name="Jeff Calder", email="jwcalder@umn.edu" },
+]
+description = "Python package for mesh processing tools developed by AMAAZE"
+readme = "README.md"
+license = {text = "MIT"}
+requires-python = ">=3.6"
+classifiers = [
+   "Programming Language :: Python :: 3",
+   "License :: OSI Approved :: MIT License",
+   "Operating System :: OS Independent",
+]
+dependencies = ['numpy',
+                'scipy',
+                'pandas',
+                'pydicom',
+                'scikit-image',
+                'sklearn',
+                'matplotlib',
+                'graphlearning',
+                'plyfile'
+]
+
+[project.urls]
+"Homepage" = "https://github.com/jwcalder/AMAAZETools"
+"Bug Tracker" = "https://github.com/jwcalder/AMAAZETools/issues"

amaazetools-0.1.0/setup.py

@@ -0,0 +1,16 @@
+from setuptools import setup, Extension
+import numpy 
+
+setup_args = dict(
+    ext_modules=[Extension('amaazetools.cextensions',
+                            sources=['src/cextensions.c',
+                                     'src/svi_computations.c',
+                                     'src/mesh_operations.c',
+                                     'src/memory_allocation.c'],
+                            include_dirs=[numpy.get_include()],
+                            extra_compile_args = ['-Ofast'],
+                            extra_link_args = ['-lm'])])
+
+setup(**setup_args)
+
+

amaazetools-0.0.8/setup.py

@@ -1,41 +0,0 @@
-#This is a setup file
-import setuptools
-import numpy
-
-
-with open("README.md", "r", encoding="utf-8") as fh:
-    long_description = fh.read()
-
-setuptools.setup(
-    name="amaazetools", 
-    version="0.0.8",
-    author="Jeff Calder",
-    author_email="jwcalder@umn.edu",
-    description="Python package for mesh processing tools developed by AMAAZE",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/jwcalder/AMAAZETools",
-    packages=['amaazetools'],
-    ext_modules=[setuptools.Extension('amaazetools.cextensions',
-                    sources=['src/cextensions.c',
-                             'src/svi_computations.c',
-                             'src/mesh_operations.c',
-                             'src/memory_allocation.c'],
-                    include_dirs=[numpy.get_include()],
-                    extra_compile_args = ['-Ofast'],
-                    extra_link_args = ['-lm'])],
-    classifiers=["Programming Language :: Python :: 3",
-                 "License :: OSI Approved :: MIT License",
-                 "Operating System :: OS Independent"],
-    install_requires=['numpy',
-                      'scipy',
-                      'pandas',
-                      'pydicom',
-                      'scikit-image',
-                      'sklearn',
-                      'matplotlib',
-                      'graphlearning',
-                      'plyfile'],
-    python_requires='>=3.6',
-)
-