antspymm 1.3.6__py3-none-any.whl → 1.3.8__py3-none-any.whl

antspymm/mm.py

@@ -154,11 +154,11 @@ def version( ):
     """
     import pkg_resources
     return {
-              'tensorflow': pkg_resources.require("tensorflow")[0].version,
-              'antspyx': pkg_resources.require("antspyx")[0].version,
-              'antspynet': pkg_resources.require("antspynet")[0].version,
-              'antspyt1w': pkg_resources.require("antspyt1w")[0].version,
-              'antspymm': pkg_resources.require("antspymm")[0].version
+              'tensorflow': pkg_resources.get_distribution("tensorflow").version,
+              'antspyx': pkg_resources.get_distribution("antspyx").version,
+              'antspynet': pkg_resources.get_distribution("antspynet").version,
+              'antspyt1w': pkg_resources.get_distribution("antspyt1w").version,
+              'antspymm': pkg_resources.get_distribution("antspymm").version
               }
 
 def nrg_filename_to_subjectvisit(s, separator='-'):
@@ -5017,8 +5017,6 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   nmdf_wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
               {'NM' : nmdf},
               col_names = ['Mean'] )
-  if verbose:
-      print( "nm done" )
 
   rr_mask = ants.mask_image( labels2nm, labels2nm, [33,34] , binarize=True )
   sn_mask = ants.mask_image( labels2nm, labels2nm, [7,9,23,25] , binarize=True )
@@ -5028,7 +5026,8 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   rravg = nm_avg_cropped[ rr_mask == 1].mean()
   snstd = nm_avg_cropped[ sn_mask == 1].std()
   rrstd = nm_avg_cropped[ rr_mask == 1].std()
-  snvol = np.prod( ants.get_spacing(sn_mask) ) * sn_mask.sum()
+  vol_element = np.prod( ants.get_spacing(sn_mask) )
+  snvol = vol_element * sn_mask.sum()
 
   # get the mean voxel position of the SN
   if snvol > 0:
@@ -5037,7 +5036,24 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   else:
       sn_z = math.nan
 
-  nm_evr = antspyt1w.patch_eigenvalue_ratio( nm_avg, 512, [6,6,6], evdepth = 0.9, mask=cropper2nm )
+  nm_evr = 0.0
+  if cropper2nm.sum() > 0:
+    nm_evr = antspyt1w.patch_eigenvalue_ratio( nm_avg, 512, [6,6,6], 
+        evdepth = 0.9, mask=cropper2nm )
+
+  simg = ants.smooth_image( nm_avg_cropped, np.min(ants.get_spacing(nm_avg_cropped)) )
+  k = 2.0
+  rrthresh = (rravg + k * rrstd)
+  nmabovekthresh_mask = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
+  snvolabovethresh = vol_element * nmabovekthresh_mask.sum()
+  snintmeanabovethresh = ( simg * nmabovekthresh_mask ).mean()
+  snintsumabovethresh = ( simg * nmabovekthresh_mask ).sum()
+  
+  if verbose:
+    print( "nm vol @2std above rrmean: " + str( snvolabovethresh ) )
+    print( "nm intmean @2std above rrmean: " + str( snintmeanabovethresh ) )
+    print( "nm intsum @2std above rrmean: " + str( snintsumabovethresh ) )
+    print( "nm done" )
 
   return{
       'NM_avg' : nm_avg,
@@ -5053,6 +5069,9 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
       'NM_avg_substantianigra' : snavg,
       'NM_std_substantianigra' : snstd,
       'NM_volume_substantianigra' : snvol,
+      'NM_volume_substantianigra_above_k_thresh' : snvolabovethresh,
+      'NM_intmean_substantianigra_above_k_thresh' : snintmeanabovethresh,
+      'NM_intsum_substantianigra_above_k_thresh' : snintsumabovethresh,
       'NM_avg_refregion' : rravg,
       'NM_std_refregion' : rrstd,
       'NM_min' : nm_avg_cropped.min(),

{antspymm-1.3.6.dist-info → antspymm-1.3.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.6
+Version: 1.3.8
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
@@ -10,8 +10,8 @@ License-File: LICENSE
 Requires-Dist: h5py >=2.10.0
 Requires-Dist: numpy >=1.19.4
 Requires-Dist: pandas >=1.0.1
-Requires-Dist: antspyx
-Requires-Dist: antspynet >=0.2.5
+Requires-Dist: antspyx >=0.4.2
+Requires-Dist: antspynet >=0.2.8
 Requires-Dist: antspyt1w >=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
@@ -22,6 +22,8 @@ Requires-Dist: scikit-learn
 
 # ANTsPyMM
 
+[![CircleCI](https://dl.circleci.com/status-badge/img/gh/ANTsX/ANTsPyMM/tree/main.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/gh/ANTsX/ANTsPyMM/tree/main)
+
 ![mapping](https://i.imgur.com/qKqYjU9.jpeg)
 
 ## processing utilities for timeseries/multichannel images - mostly neuroimaging

antspymm-1.3.8.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
+antspymm/mm.py,sha256=72293DXAlbeKXj75j5d_SYeiH2uKK9-XnpZh6YLIpwY,480752
+antspymm-1.3.8.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.3.8.dist-info/METADATA,sha256=P1Q9RDLvhqAQalZfVewHpbbvTPzsYBo91cTpBtGrOSw,14866
+antspymm-1.3.8.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+antspymm-1.3.8.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.3.8.dist-info/RECORD,,

antspymm-1.3.6.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
-antspymm/mm.py,sha256=4g15BkmRyIn-ZTB7DOT9ggTDt-Ma3be44zKpCTALikY,479806
-antspymm-1.3.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.3.6.dist-info/METADATA,sha256=CRZs-L_1fv4rQPaKsMDPK0_9SHr6BLEyieHo30fLctw,14684
-antspymm-1.3.6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-antspymm-1.3.6.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.3.6.dist-info/RECORD,,