antspymm 1.6.0__tar.gz → 1.6.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (70) hide show
  1. {antspymm-1.6.0 → antspymm-1.6.1}/PKG-INFO +1 -1
  2. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm/mm.py +1 -1
  3. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm.egg-info/PKG-INFO +1 -1
  4. {antspymm-1.6.0 → antspymm-1.6.1}/docs/mm_csv_localint.py +2 -2
  5. {antspymm-1.6.0 → antspymm-1.6.1}/pyproject.toml +1 -1
  6. {antspymm-1.6.0 → antspymm-1.6.1}/MANIFEST.in +0 -0
  7. {antspymm-1.6.0 → antspymm-1.6.1}/README.md +0 -0
  8. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm/__init__.py +0 -0
  9. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm.egg-info/SOURCES.txt +0 -0
  10. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm.egg-info/dependency_links.txt +0 -0
  11. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm.egg-info/requires.txt +0 -0
  12. {antspymm-1.6.0 → antspymm-1.6.1}/antspymm.egg-info/top_level.txt +0 -0
  13. {antspymm-1.6.0 → antspymm-1.6.1}/docs/adni_rsfmri_2_nrg_conversion.py +0 -0
  14. {antspymm-1.6.0 → antspymm-1.6.1}/docs/antspymm_annotated_output_tree.pages +0 -0
  15. {antspymm-1.6.0 → antspymm-1.6.1}/docs/antspymm_annotated_output_tree.txt +0 -0
  16. {antspymm-1.6.0 → antspymm-1.6.1}/docs/antspymm_data_dictionary.csv +0 -0
  17. {antspymm-1.6.0 → antspymm-1.6.1}/docs/aslprep_perfusion_run_localint.py +0 -0
  18. {antspymm-1.6.0 → antspymm-1.6.1}/docs/bids_2_nrg.py +0 -0
  19. {antspymm-1.6.0 → antspymm-1.6.1}/docs/bids_cohort_example.py +0 -0
  20. {antspymm-1.6.0 → antspymm-1.6.1}/docs/bind_mm_wide.R +0 -0
  21. {antspymm-1.6.0 → antspymm-1.6.1}/docs/blind_qc.Rmd +0 -0
  22. {antspymm-1.6.0 → antspymm-1.6.1}/docs/blind_qc.html +0 -0
  23. {antspymm-1.6.0 → antspymm-1.6.1}/docs/blind_qc.py +0 -0
  24. {antspymm-1.6.0 → antspymm-1.6.1}/docs/convert_adni_dti_to_nrg.R +0 -0
  25. {antspymm-1.6.0 → antspymm-1.6.1}/docs/deepnbm.jpg +0 -0
  26. {antspymm-1.6.0 → antspymm-1.6.1}/docs/deformation_gradient_reo.py +0 -0
  27. {antspymm-1.6.0 → antspymm-1.6.1}/docs/describe_mm_data.R +0 -0
  28. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dipy_dti_recon.py +0 -0
  29. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dti_distortion_correction_voxelwise_varying_bvectors_example.py +0 -0
  30. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dti_recon.py +0 -0
  31. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dti_reconstruction_voxelwise_varying_bvectors_localint.py +0 -0
  32. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dti_reg.py +0 -0
  33. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dwi_rebasing.py +0 -0
  34. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dwi_run.py +0 -0
  35. {antspymm-1.6.0 → antspymm-1.6.1}/docs/dwi_run_ptbp_scrub.py +0 -0
  36. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ex_rsfmri_run_minimal_ptbp.py +0 -0
  37. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ex_sr.py +0 -0
  38. {antspymm-1.6.0 → antspymm-1.6.1}/docs/example_antspymm_output.csv +0 -0
  39. {antspymm-1.6.0 → antspymm-1.6.1}/docs/example_run_from_directory.py +0 -0
  40. {antspymm-1.6.0 → antspymm-1.6.1}/docs/flair_run_localint.py +0 -0
  41. {antspymm-1.6.0 → antspymm-1.6.1}/docs/joint_dti_recon_localint.py +0 -0
  42. {antspymm-1.6.0 → antspymm-1.6.1}/docs/make_dict_table.Rmd +0 -0
  43. {antspymm-1.6.0 → antspymm-1.6.1}/docs/make_dict_table.html +0 -0
  44. {antspymm-1.6.0 → antspymm-1.6.1}/docs/mm.py +0 -0
  45. {antspymm-1.6.0 → antspymm-1.6.1}/docs/mm_csv_ex_2.py +0 -0
  46. {antspymm-1.6.0 → antspymm-1.6.1}/docs/mm_nrg.py +0 -0
  47. {antspymm-1.6.0 → antspymm-1.6.1}/docs/nrg_cohort_example.py +0 -0
  48. {antspymm-1.6.0 → antspymm-1.6.1}/docs/parallel_study_aggregation_example.py +0 -0
  49. {antspymm-1.6.0 → antspymm-1.6.1}/docs/perfusion_ptbp.py +0 -0
  50. {antspymm-1.6.0 → antspymm-1.6.1}/docs/perfusion_run_nnl.py +0 -0
  51. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ppmi_step1_blind_qc.py +0 -0
  52. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ppmi_step2_outlierness.py +0 -0
  53. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ppmi_step3_mm_nrg_csv.py +0 -0
  54. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ppmi_step4_aggregate.py +0 -0
  55. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ptbp_nrg.py +0 -0
  56. {antspymm-1.6.0 → antspymm-1.6.1}/docs/roi_visualization.py +0 -0
  57. {antspymm-1.6.0 → antspymm-1.6.1}/docs/roi_visualization_ppmi.py +0 -0
  58. {antspymm-1.6.0 → antspymm-1.6.1}/docs/rsfmri_run_minimal_localint.py +0 -0
  59. {antspymm-1.6.0 → antspymm-1.6.1}/docs/run_local_integration_scripts.py +0 -0
  60. {antspymm-1.6.0 → antspymm-1.6.1}/docs/run_mm_example.sh +0 -0
  61. {antspymm-1.6.0 → antspymm-1.6.1}/docs/template_overlays.py +0 -0
  62. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ukbb_rsfmri.py +0 -0
  63. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ukbb_to_nrg_processing.py +0 -0
  64. {antspymm-1.6.0 → antspymm-1.6.1}/docs/ukbb_to_nrg_processing2.py +0 -0
  65. {antspymm-1.6.0 → antspymm-1.6.1}/docs/visualize_tractogram.py +0 -0
  66. {antspymm-1.6.0 → antspymm-1.6.1}/setup.cfg +0 -0
  67. {antspymm-1.6.0 → antspymm-1.6.1}/tests/test_loop.py +0 -0
  68. {antspymm-1.6.0 → antspymm-1.6.1}/tests/test_nrg_validation.py +0 -0
  69. {antspymm-1.6.0 → antspymm-1.6.1}/tests/test_reference_run.py +0 -0
  70. {antspymm-1.6.0 → antspymm-1.6.1}/tests/voxelwise_bvec_dti_recon_test.py +0 -0
{antspymm-1.6.0 → antspymm-1.6.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: antspymm
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- Version: 1.6.0
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+ Version: 1.6.1
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  Summary: multi-channel/time-series medical image processing with antspyx
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  Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
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  License: Apache-2.0
{antspymm-1.6.0 → antspymm-1.6.1}/antspymm/mm.py RENAMED
@@ -4557,7 +4557,7 @@ def joint_dti_recon(
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  maskInRightSpace = ants.image_physical_space_consistency( brain_mask, reference_B0 )
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  if not maskInRightSpace :
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  raise ValueError('not maskInRightSpace ... provided brain mask should be in reference_B0 space')
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- brainmaske = ants.iMath( maskInRightSpace, "ME", 2 )
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+ brainmaske = ants.iMath( brain_mask, "ME", 2 )
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  if img_RL is not None :
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  if verbose:
{antspymm-1.6.0 → antspymm-1.6.1}/antspymm.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: antspymm
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- Version: 1.6.0
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+ Version: 1.6.1
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  Summary: multi-channel/time-series medical image processing with antspyx
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  Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
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  License: Apache-2.0
{antspymm-1.6.0 → antspymm-1.6.1}/docs/mm_csv_localint.py RENAMED
@@ -142,7 +142,7 @@ candidate_rdirs = [
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  rdir = find_data_dir( candidate_rdirs, allow_download="~/Downloads" )
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  print(f"Using data directory: {rdir}")
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- nthreads = str(1)
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+ nthreads = str(8)
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  os.environ["TF_NUM_INTEROP_THREADS"] = nthreads
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  os.environ["TF_NUM_INTRAOP_THREADS"] = nthreads
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  os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = nthreads
@@ -156,7 +156,7 @@ import random
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  import re
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  mydir = rdir + "PPMI/"
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  outdir = re.sub( 'nrgdata_test', 'antspymmoutput_repro', rdir )
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- # outdir = re.sub( 'nrgdata_test', 'antspymmoutput', rdir )
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+ outdir = re.sub( 'nrgdata_test', 'antspymmoutput', rdir )
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  #####################
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  import antspymm #####
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  import pandas as pd #
{antspymm-1.6.0 → antspymm-1.6.1}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "antspymm"
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- version = "1.6.0"
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+ version = "1.6.1"
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  description = "multi-channel/time-series medical image processing with antspyx"
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  readme = "README.md"
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  requires-python = ">=3.9"
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{antspymm-1.6.0 → antspymm-1.6.1}/docs/dwi_run.py RENAMED
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{antspymm-1.6.0 → antspymm-1.6.1}/docs/mm_csv_ex_2.py RENAMED
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{antspymm-1.6.0 → antspymm-1.6.1}/docs/mm_nrg.py RENAMED
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{antspymm-1.6.0 → antspymm-1.6.1}/docs/ptbp_nrg.py RENAMED
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{antspymm-1.6.0 → antspymm-1.6.1}/docs/ukbb_rsfmri.py RENAMED
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{antspymm-1.6.0 → antspymm-1.6.1}/setup.cfg RENAMED
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{antspymm-1.6.0 → antspymm-1.6.1}/tests/test_loop.py RENAMED
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