amaazetools 0.1.9__tar.gz → 0.2.1__tar.gz

{amaazetools-0.1.9/amaazetools.egg-info → amaazetools-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: amaazetools
-Version: 0.1.9
+Version: 0.2.1
 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-0.1.9 → amaazetools-0.2.1}/amaazetools/dicom.py

@@ -341,7 +341,7 @@ def imshow(J):
     plt.figure()
     plt.imshow(J, cmap='gray')
 
-def surface_bones(directory, iso=2500, write_gif=False):
+def surface_bones(directory, iso=2500, write_gif=False, mirror=False):
     """ Processes all npz files in directory creating surface and saving to a ply file.
 
         Parameters
@@ -352,6 +352,8 @@ def surface_bones(directory, iso=2500, write_gif=False):
             Iso level to be used for surfacing.
         write_gif : bool (optional), default=False
             Whether to output rotating gifs for each object. Requires mayavi, which can be hard to install.
+        mirror : bool (optional), default=False
+            Whether to mirror bones when surfacing.
 
         Returns
         -------
@@ -367,6 +369,9 @@ def surface_bones(directory, iso=2500, write_gif=False):
             #Rescale image to account for different dx/dz dimensions
             J = rescale(I.astype(float),(dz/dx,1,1),mode='constant')
 
+            if mirror:
+                J = J[::-1,:,:]
+
             #Marching cubes for isosurface
             iso_level = iso
             verts,faces,normals,values = tm.marching_cubes(J,iso_level)
@@ -486,9 +491,10 @@ 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)
@@ -870,7 +876,7 @@ def seg_adjacency_matrix(u):
     return M,X,Y
 
 
-def surfacing_subproc(filename,directory,iso_level,write_gif=False):
+def surfacing_subproc(filename,directory,iso_level,write_gif=False,miror=False):
     
     print('Loading '+filename+'...')
     M = np.load(os.path.join(directory,filename))
@@ -878,6 +884,9 @@ def surfacing_subproc(filename,directory,iso_level,write_gif=False):
     
     #Rescale image to account for different dx/dz dimensions
     J = rescale(I.astype(float),(dz/dx,1,1),mode='constant')
+
+    if mirror:
+        J = J[::-1,:,:]
     
     try: 
         verts,faces,normals,values = tm.marching_cubes(J,iso_level)

{amaazetools-0.1.9 → amaazetools-0.2.1/amaazetools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: amaazetools
-Version: 0.1.9
+Version: 0.2.1
 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-0.1.9 → amaazetools-0.2.1}/pyproject.toml

@@ -9,7 +9,7 @@ packages = ['amaazetools']
 
 [project]
 name = "amaazetools"
-version = "0.1.9"
+version = "0.2.1"
 authors = [
   { name="Jeff Calder", email="jwcalder@umn.edu" },
 ]