antspymm 1.3.5__tar.gz → 1.3.6__tar.gz

{antspymm-1.3.5/antspymm.egg-info → antspymm-1.3.6}/PKG-INFO

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.5
+Version: 1.3.6
 Summary: multi-channel/time-series medical image processing with antspyx
-Home-page: https://github.com/stnava/ANTsPyMM
-Author: Avants, Gosselin, Tustison, Reardon
-Author-email: stnava@gmail.com
+Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
 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: antspyt1w>=0.2.3
+Requires-Dist: antspynet>=0.2.5
+Requires-Dist: antspyt1w>=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -35,7 +35,7 @@ production environments.
 install the `dev` version by calling (within the source directory):
 
 ```
-python setup.py install
+python3 -m  build .
 ```
 
 or install the latest release via 
@@ -450,9 +450,12 @@ ssl._create_default_https_context = ssl._create_unverified_context
 
 ## to publish a release
 
+before doing this - make sure you have a recent run of `pip-compile pyproject.toml`
+
 ```
 rm -r -f build/ antspymm.egg-info/ dist/
-python3 setup.py sdist bdist_wheel
-twine upload --repository antspymm dist/*
+python3 -m  build .
+python3 -m pip install --upgrade twine
+python3 -m twine upload --repository antspymm dist/*
 ```
 

{antspymm-1.3.5 → antspymm-1.3.6}/README.md

@@ -13,7 +13,7 @@ production environments.
 install the `dev` version by calling (within the source directory):
 
 ```
-python setup.py install
+python3 -m  build .
 ```
 
 or install the latest release via 
@@ -428,9 +428,12 @@ ssl._create_default_https_context = ssl._create_unverified_context
 
 ## to publish a release
 
+before doing this - make sure you have a recent run of `pip-compile pyproject.toml`
+
 ```
 rm -r -f build/ antspymm.egg-info/ dist/
-python3 setup.py sdist bdist_wheel
-twine upload --repository antspymm dist/*
+python3 -m  build .
+python3 -m pip install --upgrade twine
+python3 -m twine upload --repository antspymm dist/*
 ```
 

{antspymm-1.3.5 → antspymm-1.3.6}/antspymm/mm.py

@@ -7979,14 +7979,13 @@ def mm_csv(
         t1wide.to_csv( hierfn + 'mmwide.csv' )
     ################# read the hierarchical data ###############################
     # over-write the rbp data with a consistent and recent approach ############
-    myx = antspyt1w.inspect_raw_t1( t1, hierfn + 'rbp' , option='both' ) 
+    myx = antspyt1w.inspect_raw_t1( t1, hierfn + 'rbp' , option='both' )
+    myx['brain'].to_csv( hierfn + 'rbp.csv', index=False )
+    myx['brain'].to_csv( hierfn + 'rbpbrain.csv', index=False )
     del myx
     hier = antspyt1w.read_hierarchical( hierfn )
-    if exists( hierfn + 'mmwide.csv' ) :
-        t1wide = pd.read_csv( hierfn + 'mmwide.csv' )
-    elif not testloop:
-        t1wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
-                hier['dataframes'], identifier=None )
+    t1wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
+        hier['dataframes'], identifier=None )
     rgrade = str( t1wide['resnetGrade'].iloc[0] )
     if t1wide['resnetGrade'].iloc[0] < 0.20:
         warnings.warn('T1w quality check indicates failure: ' + rgrade + " will not process." )
@@ -8087,6 +8086,8 @@ def mm_csv(
                 print( 'example image name is : '  )
                 print( myimgsr )
             if overmodX == 'NM2DMT':
+                dowrite = True
+                visualize = True
                 subjectpropath = os.path.dirname( mydoc['outprefix'] )
                 if verbose:
                     print("subjectpropath is")
@@ -8146,16 +8147,17 @@ def mm_csv(
                         print(f"antspymmerror occurred while processing {overmodX}: {e}")
                         pass
                     if not test_run:
-                        write_mm( output_prefix=mymm, mm=tabPro, mm_norm=normPro, t1wide=None, separator=mysep )
-                        nmpro = tabPro['NM']
-                        mysl = range( nmpro['NM_avg'].shape[2] )
-                    if visualize:
-                        mysl = range( nmpro['NM_avg'].shape[2] )
-                        ants.plot( nmpro['NM_avg'],  nmpro['t1_to_NM'], slices=mysl, axis=2, title='nm + t1', filename=mymm+mysep+"NMavg.png" )
-                        mysl = range( nmpro['NM_avg_cropped'].shape[2] )
-                        ants.plot( nmpro['NM_avg_cropped'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop', filename=mymm+mysep+"NMavgcrop.png" )
-                        ants.plot( nmpro['NM_avg_cropped'], nmpro['t1_to_NM'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop + t1', filename=mymm+mysep+"NMavgcropt1.png" )
-                        ants.plot( nmpro['NM_avg_cropped'], nmpro['NM_labels'], axis=2, slices=mysl, title='nm crop + labels', filename=mymm+mysep+"NMavgcroplabels.png" )
+                        if dowrite:
+                            write_mm( output_prefix=mymm, mm=tabPro,
+                                mm_norm=normPro, t1wide=None, separator=mysep )
+                        if visualize :
+                            nmpro = tabPro['NM']
+                            mysl = range( nmpro['NM_avg'].shape[2] )
+                            ants.plot( nmpro['NM_avg'],  nmpro['t1_to_NM'], slices=mysl, axis=2, title='nm + t1', filename=mymm+mysep+"NMavg.png" )
+                            mysl = range( nmpro['NM_avg_cropped'].shape[2] )
+                            ants.plot( nmpro['NM_avg_cropped'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop', filename=mymm+mysep+"NMavgcrop.png" )
+                            ants.plot( nmpro['NM_avg_cropped'], nmpro['t1_to_NM'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop + t1', filename=mymm+mysep+"NMavgcropt1.png" )
+                            ants.plot( nmpro['NM_avg_cropped'], nmpro['NM_labels'], axis=2, slices=mysl, title='nm crop + labels', filename=mymm+mysep+"NMavgcroplabels.png" )
             else :
                 if len( myimgsr ) > 0:
                     dowrite=False

{antspymm-1.3.5 → antspymm-1.3.6/antspymm.egg-info}/PKG-INFO

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.5
+Version: 1.3.6
 Summary: multi-channel/time-series medical image processing with antspyx
-Home-page: https://github.com/stnava/ANTsPyMM
-Author: Avants, Gosselin, Tustison, Reardon
-Author-email: stnava@gmail.com
+Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
 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: antspyt1w>=0.2.3
+Requires-Dist: antspynet>=0.2.5
+Requires-Dist: antspyt1w>=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -35,7 +35,7 @@ production environments.
 install the `dev` version by calling (within the source directory):
 
 ```
-python setup.py install
+python3 -m  build .
 ```
 
 or install the latest release via 
@@ -450,9 +450,12 @@ ssl._create_default_https_context = ssl._create_unverified_context
 
 ## to publish a release
 
+before doing this - make sure you have a recent run of `pip-compile pyproject.toml`
+
 ```
 rm -r -f build/ antspymm.egg-info/ dist/
-python3 setup.py sdist bdist_wheel
-twine upload --repository antspymm dist/*
+python3 -m  build .
+python3 -m pip install --upgrade twine
+python3 -m twine upload --repository antspymm dist/*
 ```
 

{antspymm-1.3.5 → antspymm-1.3.6}/antspymm.egg-info/SOURCES.txt

@@ -1,13 +1,12 @@
 LICENSE
 MANIFEST.in
 README.md
-setup.py
+pyproject.toml
 antspymm/__init__.py
 antspymm/mm.py
 antspymm.egg-info/PKG-INFO
 antspymm.egg-info/SOURCES.txt
 antspymm.egg-info/dependency_links.txt
-antspymm.egg-info/not-zip-safe
 antspymm.egg-info/requires.txt
 antspymm.egg-info/top_level.txt
 docs/adni_rsfmri_2_nrg_conversion.py
@@ -23,7 +22,9 @@ 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
@@ -36,6 +37,7 @@ tests/mm.py
 tests/mm_nrg.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
@@ -48,6 +50,7 @@ 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

{antspymm-1.3.5 → antspymm-1.3.6}/antspymm.egg-info/requires.txt

@@ -2,7 +2,8 @@ h5py>=2.10.0
 numpy>=1.19.4
 pandas>=1.0.1
 antspyx
-antspyt1w>=0.2.3
+antspynet>=0.2.5
+antspyt1w>=0.9.3
 pathlib
 dipy
 nibabel

antspymm-1.3.6/docs/release_notes.py

@@ -0,0 +1,50 @@
+
+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

@@ -0,0 +1,28 @@
+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/pyproject.toml

@@ -0,0 +1,32 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "antspymm"
+version = "1.3.6"
+description = "multi-channel/time-series medical image processing with antspyx"
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "Apache 2.0" }
+authors = [
+    { name = "Avants, Gosselin, Tustison, Reardon", email = "stnava@gmail.com" }
+]
+
+dependencies = [
+    "h5py>=2.10.0",
+    "numpy>=1.19.4",
+    "pandas>=1.0.1",
+    "antspyx",
+    "antspynet>=0.2.5",
+    "antspyt1w>=0.9.3",
+    "pathlib",
+    "dipy",
+    "nibabel",
+    "scipy",
+    "siq",
+    "scikit-learn"
+]
+
+[tool.setuptools.packages]
+find = { include = ["antspymm"] }

antspymm-1.3.6/tests/test_00_setup.py

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

{antspymm-1.3.5 → antspymm-1.3.6}/tests/test_deformation_gradient_reo.py

@@ -14,6 +14,8 @@ import tensorflow as tf
 from tempfile import mktemp
 import numpy as np
 import antspymm
+import sys
+sys.exit(0) # this is not an actual test that we want to run regularly
 print(" Load in JHU atlas and labels ")
 ex_path = os.path.expanduser( "~/.antspyt1w/" )
 ex_path_mm = os.path.expanduser( "~/.antspymm/" )

{antspymm-1.3.5 → antspymm-1.3.6}/tests/test_dti_recon.py

@@ -3,4 +3,6 @@ import antspymm
 img1 = ants.image_read( antspymm.get_data( "I1499279_Anon_20210819142214_5", target_extension=".nii.gz") )
 bvec = antspymm.get_data( "I1499279_Anon_20210819142214_5", target_extension=".bvec")
 bval = antspymm.get_data( "I1499279_Anon_20210819142214_5", target_extension=".bval")
-dd = antspymm.dipy_dti_recon( img1, bval, bvec, motion_correct=True, mask_dilation=0 )
+dd = antspymm.dipy_dti_recon( img1, bval, bvec )
+import sys
+sys.exit(0)

antspymm-1.3.6/tests/test_perfusion_ptbp2.py

@@ -0,0 +1,36 @@
+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' )

antspymm-1.3.5/antspymm.egg-info/not-zip-safe

@@ -1 +0,0 @@
-

antspymm-1.3.5/setup.py

@@ -1,30 +0,0 @@
-
-from setuptools import setup, find_packages
-
-long_description = open("README.md").read()
-
-requirements = [
-      "h5py>=2.10.0",
-      "numpy>=1.19.4",
-      "pandas>=1.0.1",
-      "antspyx",
-      "antspyt1w>=0.2.3",
-      "pathlib",
-      "dipy",
-      "nibabel",
-      "scipy",
-      "siq",
-      "scikit-learn"]
-
-setup(name='antspymm',
-      version='1.3.5',
-      description='multi-channel/time-series medical image processing with antspyx',
-      long_description=long_description,
-      long_description_content_type="text/markdown; charset=UTF-8; variant=GFM",
-      url='https://github.com/stnava/ANTsPyMM',
-      author='Avants, Gosselin, Tustison, Reardon',
-      author_email='stnava@gmail.com',
-      license='Apache 2.0',
-      install_requires=requirements,
-      packages=['antspymm'],
-      zip_safe=False)