antspymm 1.3.6__tar.gz → 1.3.8__tar.gz

{antspymm-1.3.6/antspymm.egg-info → antspymm-1.3.8}/PKG-INFO

@@ -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-1.3.6 → antspymm-1.3.8}/README.md

@@ -1,5 +1,7 @@
 # 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-1.3.6 → antspymm-1.3.8}/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 → antspymm-1.3.8/antspymm.egg-info}/PKG-INFO

@@ -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-1.3.6 → antspymm-1.3.8}/antspymm.egg-info/SOURCES.txt

@@ -22,9 +22,7 @@ docs/make_dict_table.Rmd
 docs/make_dict_table.html
 docs/nrg_cohort_example.py
 docs/ptbp_nrg.py
-docs/release_notes.py
 docs/roi_visualization.py
-docs/roi_visualization_limbic.py
 docs/roi_visualization_ppmi.py
 docs/step1_blind_qc.py
 docs/step2_outlierness.py
@@ -32,28 +30,27 @@ docs/step3_mm_nrg_csv.py
 docs/step4_aggregate.py
 docs/ukbb_to_nrg_processing.py
 docs/ukbb_to_nrg_processing2.py
+tests/bids_2_nrg.py
 tests/blind_qc.py
+tests/deformation_gradient_reo.py
+tests/dti_recon.py
+tests/dti_reg.py
+tests/dwi_rebasing.py
+tests/dwi_run.py
+tests/dwi_run_ptbp_scrub.py
+tests/flair_run.py
+tests/joint_dti_recon.py
 tests/mm.py
+tests/mm_csv.py
 tests/mm_nrg.py
+tests/nrg_validation.py
 tests/outlierness.py
 tests/parallel_study_aggregation_example.py
-tests/test_00_setup.py
-tests/test_bids_2_nrg.py
-tests/test_deformation_gradient_reo.py
-tests/test_dti_recon.py
-tests/test_dti_reg.py
-tests/test_dwi_rebasing.py
-tests/test_dwi_run.py
-tests/test_dwi_run_ptbp_scrub.py
-tests/test_flair_run.py
-tests/test_joint_dti_recon.py
-tests/test_mm_csv.py
-tests/test_nrg_validation.py
-tests/test_perfusion_ptbp.py
-tests/test_perfusion_ptbp2.py
-tests/test_perfusion_run.py
-tests/test_rsfmri_run.py
-tests/test_rsfmri_run_minimal.py
-tests/test_ukbb_rsfmri.py
+tests/perfusion_ptbp.py
+tests/perfusion_run.py
+tests/rsfmri_run.py
+tests/rsfmri_run_minimal.py
+tests/test_reference_run.py
 tests/testsr.py
+tests/ukbb_rsfmri.py
 tests/visualize_tractogram.py

{antspymm-1.3.6 → antspymm-1.3.8}/antspymm.egg-info/requires.txt

@@ -1,8 +1,8 @@
 h5py>=2.10.0
 numpy>=1.19.4
 pandas>=1.0.1
-antspyx
-antspynet>=0.2.5
+antspyx>=0.4.2
+antspynet>=0.2.8
 antspyt1w>=0.9.3
 pathlib
 dipy

{antspymm-1.3.6 → antspymm-1.3.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "antspymm"
-version = "1.3.6"
+version = "1.3.8"
 description = "multi-channel/time-series medical image processing with antspyx"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -17,8 +17,8 @@ dependencies = [
     "h5py>=2.10.0",
     "numpy>=1.19.4",
     "pandas>=1.0.1",
-    "antspyx",
-    "antspynet>=0.2.5",
+    "antspyx>=0.4.2",
+    "antspynet>=0.2.8",
     "antspyt1w>=0.9.3",
     "pathlib",
     "dipy",

antspymm-1.3.8/tests/test_reference_run.py

@@ -0,0 +1,20 @@
+import sys, os
+import unittest
+os.environ["TF_NUM_INTEROP_THREADS"] = "8"
+os.environ["TF_NUM_INTRAOP_THREADS"] = "8"
+os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "8"
+import tempfile
+import shutil
+import antspyt1w
+import antspynet
+import antspymm
+import ants
+import re
+import pandas as pd
+# just test that things loaded ok
+if os.getenv('CI') == 'true' and os.getenv('CIRCLECI') == 'true':
+    def test_simple():
+        assert os.getenv('CI') == 'true' and os.getenv('CIRCLECI') == 'true'
+else:
+    def test_simple():
+        assert os.getenv('CI') != 'true' and os.getenv('CIRCLECI') != 'true'

antspymm-1.3.6/docs/release_notes.py

@@ -1,50 +0,0 @@
-
-import os
-from git import Repo
-from github import Github
-
-def generate_release_notes(repo_path, from_tag, to_tag, github_repo_name, github_token, release_notes_file):
-    """
-    Generates release notes by extracting commit messages between two tags and fetching closed issues from GitHub.
-
-    Parameters:
-    - repo_path (str): Local path to the Git repository.
-    - from_tag (str): Tag to start collecting commits.
-    - to_tag (str): Tag to end collecting commits.
-    - github_repo_name (str): Full GitHub repository name (e.g., 'username/repository').
-    - github_token (str): GitHub access token for authentication.
-    - release_notes_file (str): File path to save the release notes.
-    """
-    # Extract commits
-    repo = Repo(repo_path)
-    commits = list(repo.iter_commits(f'{from_tag}...{to_tag}'))
-    commit_messages = [commit.message.strip() for commit in commits]
-
-    # Fetch issues from GitHub
-    g = Github(github_token)
-    repo = g.get_repo(github_repo_name)
-    issues = repo.get_issues(state='closed')
-    issue_details = [(issue.number, issue.title) for issue in issues if issue.pull_request is None]
-
-    # Write to release notes file
-    with open(release_notes_file, 'w') as file:
-        file.write('Release Notes:\n\n')
-        file.write('Features and Enhancements:\n')
-        for message in commit_messages:
-            file.write(f'- {message}\n')
-        file.write('\nFixed Issues:\n')
-        for issue in issue_details:
-            file.write(f'- Issue #{issue[0]}: {issue[1]}\n')
-
-    print(f"Release notes saved to {release_notes_file}")
-
-# Example usage
-repo_path = '/path/to/your/repo'
-from_tag = 'v1.0.0'
-to_tag = 'v1.1.0'
-github_repo_name = 'username/repo'
-github_token = 'your_github_token'
-release_notes_file = 'release_notes.md'
-
-generate_release_notes(repo_path, from_tag, to_tag, github_repo_name, github_token, release_notes_file)
-

antspymm-1.3.6/docs/roi_visualization_limbic.py

@@ -1,28 +0,0 @@
-import ants
-import pandas as pd
-import numpy as np
-import antspymm
-
-
-# Example file paths and output prefix
-x='dtPC12'
-statistical_file_path="/tmp/"+x+".csv"
-data_dictionary_path = "~/code/ANTsPyMM/docs/antspymm_data_dictionary.csv"
-output_prefix = '/tmp/vizit_'+x
-edge_image_path = '~/.antspymm/PPMI_template0_edge.nii.gz'
-edge_image_path = '~/.antspymm/PPMI_template0_brain.nii.gz'
-brain_image = ants.image_read( edge_image_path )
-brain_image_t = ants.iMath( brain_image, 'TruncateIntensity', 0.002, 0.99)
-# Call the function
-zz = pd.read_csv( statistical_file_path )
-ocols = zz.keys()
-
-qqq = zz.copy()
-qqq['anat'] = qqq['anat'].str.replace(r'(vol_|thk_|LRAVG_|_LRAVG|Asym_|_Asym|volAsym|volLRAVG|thkAsym|thkLRAVG)', '', regex=True)
-# olimg = antspymm.brainmap_figure(qqq, data_dictionary_path, output_prefix + myco, brain_image_t, nslices=21, black_bg=False, axes=[1], fixed_overlay_range=[-1.0,1.0],verbose=True )
-
-qqq['anat'] = qqq['anat'].str.replace(r'(DTI_mean_fa_|DTI_mean_md.|DTI_mean_md_|.LRAVG.)', '', regex=True)
-
-olimg = antspymm.brainmap_figure(qqq, data_dictionary_path, output_prefix, brain_image_t, nslices=21, black_bg=True,     crop=0,        overlay_cmap='winter', fixed_overlay_range=[0,1.],verbose=True )
-
-ants.image_write( olimg, '/tmp/'+x+'.nii.gz' )

antspymm-1.3.6/tests/test_00_setup.py

@@ -1,7 +0,0 @@
-import ants
-import antspyt1w
-import antspymm
-import sys
-antspyt1w.get_data()
-antspymm.get_data()
-sys.exit(0)

antspymm-1.3.6/tests/test_perfusion_ptbp2.py

@@ -1,36 +0,0 @@
-import sys, os
-os.environ["TF_NUM_INTEROP_THREADS"] = "8"
-os.environ["TF_NUM_INTRAOP_THREADS"] = "8"
-os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "8"
-import tempfile
-import shutil
-import tensorflow as tf
-import antspymm
-import antspyt1w
-import antspynet
-import ants
-import numpy as np
-from scipy.stats import median_abs_deviation
-import math
-import statsmodels.api as sm
-t1fn = "/Users/stnava/data/PTBP/images/PEDS049/20110217//Anatomy/PEDS049_20110217_mprage_t1.nii.gz"
-idpfn = "/Users/stnava/data/PTBP/images/PEDS049/20110217//PCASL/PEDS049_20110217_pcasl_1.nii.gz"
-if not 'dkt' in globals():
-  t1head = ants.image_read( t1fn ).n3_bias_field_correction( 8 ).n3_bias_field_correction( 4 )
-  t1bxt = antspynet.brain_extraction( t1head, 't1' ).threshold_image( 0.3, 1.0 )
-  t1 = t1bxt * t1head
-  t1seg = antspynet.deep_atropos( t1head )
-  t1segmentation = t1seg['segmentation_image']
-  dkt = antspynet.desikan_killiany_tourville_labeling( t1head )
-#################
-type_of_transform='Rigid'
-tc='alternating'
-fmri = ants.image_read( idpfn )
-print("do perf")
-perf = antspymm.bold_perfusion( fmri, t1head, t1, 
-  t1segmentation, dkt, robust=True, verbose=True )
-##################
-ants.plot( perf['cbf'], axis=2, crop=True )
-# ants.image_write( ants.iMath( perf['perfusion'], "Normalize" ), '/tmp/temp.nii.gz' )
-# ants.image_write( perf['motion_corrected'], '/tmp/temp2.nii.gz' )
-# ants.image_write( perf['cbf'], '/tmp/temp3ptb.nii.gz' )