antspymm 1.3.5__tar.gz → 1.3.7__tar.gz

{antspymm-1.3.5/antspymm.egg-info → antspymm-1.3.7}/PKG-INFO

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.5
+Version: 1.3.7
 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: antspyx>=0.4.2
+Requires-Dist: antspynet>=0.2.8
+Requires-Dist: antspyt1w>=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -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
@@ -35,7 +37,7 @@ 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 +452,12 @@ 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-1.3.7}/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
@@ -13,7 +15,7 @@ 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 +430,12 @@ 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-1.3.7}/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='-'):
@@ -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-1.3.7/antspymm.egg-info}/PKG-INFO

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.5
+Version: 1.3.7
 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: antspyx>=0.4.2
+Requires-Dist: antspynet>=0.2.8
+Requires-Dist: antspyt1w>=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -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
@@ -35,7 +37,7 @@ 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 +452,12 @@ 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-1.3.7}/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
@@ -36,6 +35,7 @@ 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

{antspymm-1.3.5 → antspymm-1.3.7}/antspymm.egg-info/requires.txt

@@ -1,8 +1,9 @@
 h5py>=2.10.0
 numpy>=1.19.4
 pandas>=1.0.1
-antspyx
-antspyt1w>=0.2.3
+antspyx>=0.4.2
+antspynet>=0.2.8
+antspyt1w>=0.9.3
 pathlib
 dipy
 nibabel

antspymm-1.3.7/pyproject.toml

@@ -0,0 +1,32 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "antspymm"
+version = "1.3.7"
+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>=0.4.2",
+    "antspynet>=0.2.8",
+    "antspyt1w>=0.9.3",
+    "pathlib",
+    "dipy",
+    "nibabel",
+    "scipy",
+    "siq",
+    "scikit-learn"
+]
+
+[tool.setuptools.packages]
+find = { include = ["antspymm"] }

antspymm-1.3.7/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-1.3.7}/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-1.3.7}/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-1.3.5/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)