amaazetools 0.1.8__tar.gz → 0.2.0__tar.gz

{amaazetools-0.1.8/amaazetools.egg-info → amaazetools-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: amaazetools
-Version: 0.1.8
+Version: 0.2.0
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT
@@ -21,6 +21,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
 Requires-Dist: graphlearning
 Requires-Dist: plyfile
+Dynamic: license-file
 
 # AMAAZE Tools
 

{amaazetools-0.1.8 → amaazetools-0.2.0}/amaazetools/dicom.py

@@ -486,9 +486,10 @@ def process_dicom(directory, scanlayout, CTdir='ScanOverviews', Meshdir='Meshes'
                     str_z1 = np.array2string(z1, separator=',')
                     str_z2 = np.array2string(z2, separator=',')
 
-                    df = df.append({'ScanPacket':subdir, 'Process':True, 'x1':str_x1, 'x2':str_x2, 
-                                                                         'y1':str_y1, 'y2':str_y2, 
-                                                                         'z1':str_z1, 'z2':str_z2,}, ignore_index=True)
+                    df = pd.concat([df, pd.DataFrame([{'ScanPacket':subdir, 'Process':True, 'x1':str_x1, 'x2':str_x2, 'y1':str_y1, 'y2':str_y2, 'z1':str_z1, 'z2':str_z2}])], ignore_index=True)
+                    #df = df.append({'ScanPacket':subdir, 'Process':True, 'x1':str_x1, 'x2':str_x2, 
+                    #                                                     'y1':str_y1, 'y2':str_y2, 
+                    #                                                     'z1':str_z1, 'z2':str_z2,}, ignore_index=True)
                 else: #Load chop locations from spreadsheet
 
                     x1 = np.fromstring(chopsheet['x1'][i][1:-1], sep=',').astype(int)

{amaazetools-0.1.8 → amaazetools-0.2.0}/amaazetools/trimesh.py

@@ -43,14 +43,22 @@ def marching_cubes(volume,level=None,spacing=(1,1,1)):
             points of triangulation
         t : (m,3) int
             triangles of triangulation
+        n : (n,3) float 
+            vertex normals of triangulated surface
+        val : (n) float 
+            isosurface values
     """
 
-    p,t,n,val = measure.marching_cubes(volume,level=level,spacing=spacing)
+    p,t,n,val = measure.marching_cubes(volume,level=level,spacing=spacing,allow_degenerate=False)
 
     #sometimes marching cubes produces... artifacts... so here's a very basic intro to mesh cleaning!
     #first: eliminate repeated points:
+    '''
     p,index,inv = np.unique(p,axis=0, return_index=True,return_inverse=True)
 
+    n = n[index,:]
+    val = val[index]
+
     #next: rid triangulation of non-triangles:
     t = inv[t]
     badt = (t[:,0]==t[:,1])+(t[:,1]==t[:,2])+(t[:,2]==t[:,0])
@@ -60,9 +68,13 @@ def marching_cubes(volume,level=None,spacing=(1,1,1)):
     ind = -1*np.ones(p.shape[0],int)
     uni = np.unique(t.flatten()) #these are already sorted for numpy
     ind[uni] = np.arange(uni.shape[0])
-    p = p[ind>-1,:]
-    t = ind[t]
 
+    L = ind>-1
+    p = p[L,:]
+    n = n[L,:]
+    val = val[L]
+    t = ind[t]
+    '''
     #finally, check right hand rule... this works for ~convex objects, anyway...
     #m = tm.mesh(p,t)
 
@@ -72,7 +84,7 @@ def marching_cubes(volume,level=None,spacing=(1,1,1)):
     #cent = m.points.mean(0)
     #fliporder = np.sum(tn*(tc-cent),1)<0
     #t[fliporder,1:3] = t[fliporder,2:0:-1]
-    return p,t
+    return p,t,n,val
 
 def withiness(x):
     """ Computes withiness (how well 1-D data clusters into two groups).

{amaazetools-0.1.8 → amaazetools-0.2.0/amaazetools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: amaazetools
-Version: 0.1.8
+Version: 0.2.0
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT
@@ -21,6 +21,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
 Requires-Dist: graphlearning
 Requires-Dist: plyfile
+Dynamic: license-file
 
 # AMAAZE Tools
 

{amaazetools-0.1.8 → amaazetools-0.2.0}/pyproject.toml

@@ -9,7 +9,7 @@ packages = ['amaazetools']
 
 [project]
 name = "amaazetools"
-version = "0.1.8"
+version = "0.2.0"
 authors = [
   { name="Jeff Calder", email="jwcalder@umn.edu" },
 ]