amaazetools 0.2.0__tar.gz → 0.2.2__tar.gz

{amaazetools-0.2.0/amaazetools.egg-info → amaazetools-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: amaazetools
-Version: 0.2.0
+Version: 0.2.2
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT

{amaazetools-0.2.0 → amaazetools-0.2.2}/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)
@@ -871,7 +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))
@@ -879,6 +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)
@@ -901,7 +909,7 @@ def surfacing_subproc(filename,directory,iso_level,write_gif=False):
 
 
 
-def surface_bones_parallel(directory, iso=2500, write_gif=False,error_fname='./surfacing_errors.csv',ncores='all'):
+def surface_bones_parallel(directory, iso=2500, write_gif=False, mirror=False, error_fname='./surfacing_errors.csv',ncores='all'):
     """ parallelized implementation of surface_bones with also surfacing error support.
         Processes all npz files in directory creating surface and saving to a ply file.
 
@@ -913,6 +921,8 @@ def surface_bones_parallel(directory, iso=2500, write_gif=False,error_fname='./s
             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.
         error_fname
 
         Returns
@@ -933,7 +943,7 @@ def surface_bones_parallel(directory, iso=2500, write_gif=False,error_fname='./s
     else: 
         num_cores =multiprocessing.cpu_count()
         
-    errs = Parallel(n_jobs=num_cores)(delayed(surfacing_subproc)(f,directory,iso,write_gif) for f in fnames)
+    errs = Parallel(n_jobs=num_cores)(delayed(surfacing_subproc)(f,directory,iso,mirror,write_gif) for f in fnames)
     
     errs = np.array(errs)
     errs = errs[errs!='0']

{amaazetools-0.2.0 → amaazetools-0.2.2/amaazetools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: amaazetools
-Version: 0.2.0
+Version: 0.2.2
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT

{amaazetools-0.2.0 → amaazetools-0.2.2}/pyproject.toml

@@ -9,7 +9,7 @@ packages = ['amaazetools']
 
 [project]
 name = "amaazetools"
-version = "0.2.0"
+version = "0.2.2"
 authors = [
   { name="Jeff Calder", email="jwcalder@umn.edu" },
 ]