amaazetools 0.1.0__tar.gz → 0.1.2__tar.gz

{amaazetools-0.1.0/amaazetools.egg-info → amaazetools-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: amaazetools
-Version: 0.1.0
+Version: 0.1.2
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT
@@ -17,7 +17,7 @@ Requires-Dist: scipy
 Requires-Dist: pandas
 Requires-Dist: pydicom
 Requires-Dist: scikit-image
-Requires-Dist: sklearn
+Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
 Requires-Dist: graphlearning
 Requires-Dist: plyfile

{amaazetools-0.1.0 → amaazetools-0.1.2}/amaazetools/dicom.py

@@ -869,3 +869,76 @@ def seg_adjacency_matrix(u):
 
     return M,X,Y
 
+
+def surfacing_subproc(filename,directory,iso_level,write_gif=False):
+    
+    print('Loading '+filename+'...')
+    M = np.load(os.path.join(directory,filename))
+    I = M['I']; dx = M['dx']; dz = M['dz']
+    
+    #Rescale image to account for different dx/dz dimensions
+    J = rescale(I.astype(float),(dz/dx,1,1),mode='constant')
+    
+    try: 
+        verts,faces,normals,values = measure.marching_cubes(J,iso_level)
+        mesh = tm.mesh(dx*verts,faces) #Multiplication by dx fixes units
+    
+        #Reverse orientation of triangles (marching_cubes returns inward normals)
+        mesh.flip_normals()
+    
+        #Write to ply file
+        mesh_filename = os.path.join(directory,filename[:-4]+'_iso%d'%iso_level)
+        print('Saving mesh to '+mesh_filename+'...')
+        mesh.to_ply(mesh_filename+'.ply')
+    
+        if write_gif:
+            mesh.to_gif(mesh_filename+'.gif')
+        return '0'
+    except Exception as error:
+        print('surfacing error with ', filename, ': ', error)
+        return filename
+
+
+
+def surface_bones_parallel(directory, iso=2500, write_gif=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.
+
+        Parameters
+        ----------
+        directory : str
+            Directory to work within.
+        iso : float (optional), default is 2500
+            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.
+        error_fname
+
+        Returns
+        -------
+        None
+    """
+    
+    ddd = os.listdir(directory)
+    
+    fnames = []
+    for f in ddd:
+        if f.endswith('.npz'):
+            fnames.append(f)
+    
+        
+    if isinstance(ncores,int):
+        num_cores = ncores
+    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 = np.array(errs)
+    errs = errs[errs!='0']
+    
+    if len(errs)==0:
+        print('no errors, not saving an error csv.')
+    else:
+        print('there were ' + str(len(errs)) +' errors. saving CSV to ',error_fname)              
+        pd.DataFrame(errs).to_csv(error_fname,header=False, index=False)

{amaazetools-0.1.0 → amaazetools-0.1.2/amaazetools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: amaazetools
-Version: 0.1.0
+Version: 0.1.2
 Summary: Python package for mesh processing tools developed by AMAAZE
 Author-email: Jeff Calder <jwcalder@umn.edu>
 License: MIT
@@ -17,7 +17,7 @@ Requires-Dist: scipy
 Requires-Dist: pandas
 Requires-Dist: pydicom
 Requires-Dist: scikit-image
-Requires-Dist: sklearn
+Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
 Requires-Dist: graphlearning
 Requires-Dist: plyfile

{amaazetools-0.1.0 → amaazetools-0.1.2}/amaazetools.egg-info/requires.txt

@@ -3,7 +3,7 @@ scipy
 pandas
 pydicom
 scikit-image
-sklearn
+scikit-learn
 matplotlib
 graphlearning
 plyfile

{amaazetools-0.1.0 → amaazetools-0.1.2}/pyproject.toml

@@ -9,7 +9,7 @@ packages = ['amaazetools']
 
 [project]
 name = "amaazetools"
-version = "0.1.0"
+version = "0.1.2"
 authors = [
   { name="Jeff Calder", email="jwcalder@umn.edu" },
 ]
@@ -27,7 +27,7 @@ dependencies = ['numpy',
                 'pandas',
                 'pydicom',
                 'scikit-image',
-                'sklearn',
+                'scikit-learn',
                 'matplotlib',
                 'graphlearning',
                 'plyfile'