bump version, merge pull request #27 from NiftyPET/devel

.github/workflows/comment-bot.yml

@@ -1,25 +1,23 @@
 name: Comment Bot
 on:
-  issue_comment:
-    types: [created]
-  pull_request_review_comment:
-    types: [created]
+  issue_comment: {types: [created]}
+  pull_request_review_comment: {types: [created]}
 jobs:
   tag:  # /tag <tagname> <commit>
     if: startsWith(github.event.comment.body, '/tag ')
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: React Seen
-      uses: actions/github-script@v2
+      uses: actions/github-script@v6
       with:
         script: |
-          const perm = await github.repos.getCollaboratorPermissionLevel({
+          const perm = await github.rest.repos.getCollaboratorPermissionLevel({
             owner: context.repo.owner, repo: context.repo.repo,
             username: context.payload.comment.user.login})
           post = (context.eventName == "issue_comment"
-            ? github.reactions.createForIssueComment
-            : github.reactions.createForPullRequestReviewComment)
+            ? github.rest.reactions.createForIssueComment
+            : github.rest.reactions.createForPullRequestReviewComment)
           if (!["admin", "write"].includes(perm.data.permission)){
             post({
               owner: context.repo.owner, repo: context.repo.repo,
@@ -40,12 +38,12 @@ jobs:
         BODY: ${{ github.event.comment.body }}
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
     - name: React Success
-      uses: actions/github-script@v2
+      uses: actions/github-script@v6
       with:
         script: |
           post = (context.eventName == "issue_comment"
-            ? github.reactions.createForIssueComment
-            : github.reactions.createForPullRequestReviewComment)
+            ? github.rest.reactions.createForIssueComment
+            : github.rest.reactions.createForPullRequestReviewComment)
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "rocket"})

.github/workflows/test.yml

@@ -6,11 +6,11 @@ jobs:
     runs-on: ubuntu-latest
     name: Check
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
-    - uses: actions/cache@v1
+    - uses: actions/cache@v3
       with:
         path: ~/.cache/pre-commit
         key: pre-commit|${{ env.PYSHA }}|${{ hashFiles('.pre-commit-config.yaml') }}
@@ -35,13 +35,13 @@ jobs:
     - run: pre-commit run -a --show-diff-on-failure
   test:
     if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
-    name: Test py${{ matrix.python }}
     runs-on: [self-hosted, cuda, python]
     strategy:
       matrix:
-        python: [3.7, 3.9]
+        python: [3.7, '3.10']
+    name: Test py${{ matrix.python }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Run setup-python
@@ -57,10 +57,10 @@ jobs:
     name: PyPI Deploy
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:

niftypet/nimpa/prc/imio.py

@@ -599,7 +599,7 @@ def dcmsort(folder, copy_series=False, Cnt=None, outpath=None, grouping='t+d'):
         - grouping: defines how series are recognised, i.e., either by time plus
                     series description ('t+d') or by the description only ('d'),
                     or by acquisition and series times plus series description
-                    ('a+t+d').
+                    ('a+t+d'), or using series instance unique id ('d+suid').
     '''
 
     # > insure that `folder` is Path object
@@ -648,6 +648,10 @@ def dcmsort(folder, copy_series=False, Cnt=None, outpath=None, grouping='t+d'):
         if [0x0008, 0x103e] in dhdr:
             srs_dcrp = dhdr[0x0008, 0x103e].value
 
+        srs_uid = ''
+        if [0x020, 0x00e] in dhdr:
+            srs_uid = dhdr[0x020, 0x00e].value
+
         prtcl = ''
         # > protocol
         if [0x018, 0x1030] in dhdr:
@@ -708,7 +712,7 @@ def dcmsort(folder, copy_series=False, Cnt=None, outpath=None, grouping='t+d'):
                     recognised_series = True
                     break
 
-            if grouping == 'a+t+d':
+            elif grouping == 'a+t+d':
                 if (np.array_equal(srs[s]['imorient'], ornt)
                         and np.array_equal(srs[s]['imsize'], imsz)
                         and np.array_equal(srs[s]['voxsize'], vxsz)
@@ -725,6 +729,14 @@ def dcmsort(folder, copy_series=False, Cnt=None, outpath=None, grouping='t+d'):
                     recognised_series = True
                     break
 
+            elif grouping == 'd+suid':
+                if (np.array_equal(srs[s]['imorient'], ornt)
+                        and np.array_equal(srs[s]['imsize'], imsz)
+                        and np.array_equal(srs[s]['voxsize'], vxsz)
+                        and srs[s]['series'] == srs_dcrp and srs[s]['series_uid'] == srs_uid):
+                    recognised_series = True
+                    break
+
             else:
                 raise ValueError('Unrecognised grouping option')
 
@@ -736,6 +748,8 @@ def dcmsort(folder, copy_series=False, Cnt=None, outpath=None, grouping='t+d'):
                 s = acq_time + '_' + srs_time + '_' + srs_dcrp
             elif grouping == 'd':
                 s = srs_dcrp
+            elif grouping == 'd+suid':
+                s = srs_dcrp + '_' + srs_uid[-10:]
             else:
                 raise ValueError('Unrecognised grouping option')
 
@@ -748,6 +762,7 @@ def dcmsort(folder, copy_series=False, Cnt=None, outpath=None, grouping='t+d'):
             srs[s]['tstudy'] = std_time
             srs[s]['dstudy'] = std_date
             srs[s]['series'] = srs_dcrp
+            srs[s]['series_uid'] = srs_uid
             srs[s]['protocol'] = prtcl
 
             if tinjct is not None:

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 # cuvec>=2.8.0
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4",
-            "ninst>=0.9.0", "cuvec-base", "miutil[cuda]>=0.4.0",
+            "ninst>=0.12.0", "cuvec-base", "miutil[cuda]>=0.4.0",
             "scikit-build>=0.11.0", "cmake>=3.18", "ninja"]
 
 [tool.setuptools_scm]

setup.cfg

@@ -31,6 +31,7 @@ classifiers=
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3 :: Only
     Topic :: Scientific/Engineering :: Medical Science Apps.
 [options]
@@ -39,7 +40,7 @@ setup_requires=
     setuptools>=42
     wheel
     setuptools_scm[toml]
-    ninst>=0.9.0
+    ninst>=0.12.0
     scikit-build>=0.11.0
     cmake>=3.18
     ninja

setup.py

@@ -40,7 +40,7 @@
 setup_kwargs = {
     "use_scm_version": True, "packages": find_packages(exclude=["tests"]),
     "package_data": {"niftypet": ["nimpa/auxdata/*"]}, "install_requires": [
-        'dipy>=1.3.0', 'miutil[nii]>=0.10.0', 'nibabel>=2.4.0', 'ninst>=0.4.0', 'numpy>=1.14',
+        'dipy>=1.3.0', 'miutil[nii]>=0.10.0', 'nibabel>=2.4.0', 'ninst>=0.12.0', 'numpy>=1.14',
         'pydicom>=1.0.2', 'scipy', 'setuptools', 'spm12']}
 # 'SimpleITK>=1.2.0'
 cmake_args = [