amaazetools 0.1.3__tar.gz → 0.1.5__tar.gz

{amaazetools-0.1.3/amaazetools.egg-info → amaazetools-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: amaazetools
-Version: 0.1.3
+Version: 0.1.5
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT
@@ -50,7 +50,7 @@ Email <jwcalder@umn.edu> with any questions or comments.
 
 ## Contributors
 
-Several people have contributed to the development of this software:
+Several people have contributed to the development of this software: 
 
 1. David Floeder
 2. Riley O'Neill

{amaazetools-0.1.3 → amaazetools-0.1.5}/README.md

@@ -26,7 +26,7 @@ Email <jwcalder@umn.edu> with any questions or comments.
 
 ## Contributors
 
-Several people have contributed to the development of this software:
+Several people have contributed to the development of this software: 
 
 1. David Floeder
 2. Riley O'Neill

{amaazetools-0.1.3 → amaazetools-0.1.5}/amaazetools/trimesh.py

@@ -9,13 +9,17 @@ from numpy import matlib
 from plyfile import PlyData, PlyElement
 import scipy.sparse as sparse
 import scipy.spatial as spatial
+import scipy.sparse.csgraph as csgraph
+from collections import Counter
 from skimage import measure
+from skimage.color import convert_colorspace
 from sklearn.neighbors import NearestNeighbors
 from . import svi
 from . import edge_detection
 import sys
 import urllib.request as url
 
+
 #Non-Class Specific Functions
 
 
@@ -465,6 +469,84 @@ class mesh:
             F = sparse.spdiags(1/num_adj_tri,0,self.num_verts(),self.num_verts())@F
 
         return F
+    
+    def detect_holes(self):
+        """ finds vertices bordering on holes.
+
+            Returns
+            -------
+            holes : (num_verts) boolean array
+                holes[i] = 1 if vertex i borders on a hole, else 0
+        """
+        npts = self.num_verts()
+        ntri = self.num_tri()
+
+        T = self.triangles 
+        #sparse matrices don't seem to be smart enough to remove 0's here in construction. I was going to add 1 and then remove it - no need
+
+        VT = self.tri_vert_adj()
+        
+        ntri_per_vert = VT@np.ones(ntri) #need this later
+        max_tri = int(ntri_per_vert.max())
+
+        T1 = VT.multiply(T[:,0])
+        T2 = VT.multiply(T[:,1])
+        T3 = VT.multiply(T[:,2])
+
+        I = np.hstack((T1.row,T2.row,T3.row))
+        J = np.hstack((T1.data.astype(int), T2.data.astype(int),T3.data.astype(int)))
+
+        K = sparse.coo_matrix((np.ones(len(I)), (I,J)),shape=(npts,npts)).tocsr()
+        K.data = (K.data>0).astype(int) #the construction is additive - repeated index ~> counter 
+
+        ntri_per_vert2 = (K@np.ones(npts)) -1 
+        holes = ntri_per_vert2!=ntri_per_vert
+
+        return holes
+
+
+    def con_comp(self,Q=None,returncounts=False):
+        """ extracts connected components of mesh. 
+
+            Parameters
+            ----------
+            Q : (num_verts) boolean array , default is None
+                optional array to prune edges with. If input, only edges from True to True will be considered for connectivity. 
+                If not input (or None), all edges will be used for connectivity. 
+            returncounts: boolean, default is False
+                if true, will return counts for labels.
+                
+            Returns
+            -------
+            ncomp : number of connected components.
+            labels : (num_verts) integer array
+                labels of connected components for each point. values range from 0 to ncomp-1. 
+            counts : (ncomp) integer array 
+                (optional) returns number of points under each label. array sorted from 0 to ncomp-1.
+            
+
+        """
+        T = self.triangles
+        npts = self.num_verts()
+        E = np.vstack( (T[:,[0,1]], T[:,[1,2]], T[:,[2,0]])) #edges of T
+
+        if Q is not None:
+            ll = Q[E]
+            E = E[ll[:,0]&ll[:,1],:]
+        
+        E = np.vstack( (E,E[:,[1,0]]) )
+            
+        W = sparse.coo_matrix((np.ones((np.shape(E)[0])), (E[:,0],E[:,1])),shape=(npts,npts))
+            
+        ncomp,labels = csgraph.connected_components(W,directed=False)
+
+        if returncounts:
+            co = Counter(labels)
+            co = np.array(list(co.items()))
+            counts = co[np.argsort(co[:,0]),1]
+            return ncomp,labels,counts
+        else:
+            return ncomp,labels
 
     #Returns unit normal vectors to vertices (averaging adjacent faces and normalizing)
     def vertex_normals(self):
@@ -653,13 +735,18 @@ class mesh:
         return mesh
 
     #Write a ply file
-    def to_ply(self,fname):
+    def to_ply(self,fname,c=None):
         """ Writes the mesh to a .ply file.
 
             Parameters
             ----------
             fname : str
                 The name of the .ply file to write the mesh to.
+            c : numpy array
+                Color array. If provided, then color is added to ply file.
+                If array is num_vert x 3, it is interprted as RGB colors
+                in the range 0,...,255. If the array is one dimensional 
+                of length num_vert, then the values are interpreted as hues.
         """
 
         f = open(fname,"w")
@@ -671,6 +758,11 @@ class mesh:
         f.write('property double x\n')
         f.write('property double y\n')
         f.write('property double z\n')
+        #Write color header if colors are provided
+        if c is not None:
+            f.write('property uchar red\n')
+            f.write('property uchar green\n')
+            f.write('property uchar blue\n')
         f.write('element face %u\n'%self.num_tri())
         f.write('property list int int vertex_indices\n')
         f.write('end_header\n')
@@ -678,8 +770,23 @@ class mesh:
 
         f = open(fname,"ab")
 
-        #write vertices
-        f.write(self.points.astype('float64').tobytes())
+        #If no colors are provided
+        if c is None:
+            #write vertices
+            f.write(self.points.astype('float64').tobytes())
+        #If colors are provided
+        else:
+            #If scalars provided, then convert from hue to rgb
+            if c.ndim == 1:
+                c = c - np.min(c)
+                c = c/np.max(c)
+                arr = np.vstack((c,np.ones_like(c),np.ones_like(c))).T
+                c = 255*convert_colorspace(arr,'HSV','RGB')
+
+            #write vertices
+            for i in range(self.num_verts()):
+                f.write(self.points[i,:].astype('float64').tobytes())
+                f.write(c[i,:].astype('uint8').tobytes())
 
         #write faces
         T = np.hstack((np.ones((self.num_tri(),1))*3,self.triangles)).astype(int)
@@ -688,48 +795,6 @@ class mesh:
         #close file
         f.close()
 
-    #Write a ply file
-    def write_color_ply(self,color,fname):
-        """ Writes the colored mesh to a .ply file.
-
-            Parameters
-            ----------
-            color : (num,verts,3) float array
-                An array of color data for each point.
-            fname : str
-                The name of the .ply file to write the colored mesh to.
-        """
-
-        f = open(fname,"w")
-
-        #Write header
-        f.write('ply\n')
-        f.write('format binary_little_endian 1.0\n')
-        f.write('element vertex %u\n'%self.num_verts())
-        f.write('property double x\n')
-        f.write('property double y\n')
-        f.write('property double z\n')
-        f.write('property uchar red\n')
-        f.write('property uchar green\n')
-        f.write('property uchar blue\n')
-        f.write('element face %u\n'%self.num_tri())
-        f.write('property list int int vertex_indices\n')
-        f.write('end_header\n')
-        f.close()
-
-        f = open(fname,"ab")
-
-        #write vertices
-        for i in range(self.num_verts()):
-            f.write(P[i,:].astype('float64').tobytes())
-            f.write(color[i,:].astype('uint8').tobytes())
-
-        #write faces
-        T = np.hstack((np.ones((self.num_tri(),1))*3,T)).astype(int)
-        f.write(T.astype('int32').tobytes())
-
-        #close file
-        f.close()
 
     def to_gif(self,fname,color = [],duration=7,fps=20,size=750,histeq = True):
         """ Writes rotating gif

{amaazetools-0.1.3 → amaazetools-0.1.5/amaazetools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: amaazetools
-Version: 0.1.3
+Version: 0.1.5
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT
@@ -50,7 +50,7 @@ Email <jwcalder@umn.edu> with any questions or comments.
 
 ## Contributors
 
-Several people have contributed to the development of this software:
+Several people have contributed to the development of this software: 
 
 1. David Floeder
 2. Riley O'Neill

{amaazetools-0.1.3 → amaazetools-0.1.5}/pyproject.toml

@@ -9,7 +9,7 @@ packages = ['amaazetools']
 
 [project]
 name = "amaazetools"
-version = "0.1.3"
+version = "0.1.5"
 authors = [
   { name="Jeff Calder", email="jwcalder@umn.edu" },
 ]

{amaazetools-0.1.3 → amaazetools-0.1.5}/src/cextensions.c

@@ -2,6 +2,8 @@
  *
  */
 
+
+
 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
 
 #include <Python.h>