Merge branch 'develop' of github.com:RBVI/ChimeraX into develop

RBVI · Nov 21, 2023 · 1b12cfa · 1b12cfa
2 parents 0039d75 + 896bb72
commit 1b12cfa
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Showing 4 changed files with 16 additions and 9 deletions.
diff --git a/src/bundles/dicom/src/dicom/dicom_hierarchy.py b/src/bundles/dicom/src/dicom/dicom_hierarchy.py
@@ -720,6 +720,12 @@ def affine(self):
                             , files[0].frame_positions[-1]
                             , self.files[0].mask_length
                         )
+                    else:
+                        z_axis = self._z_spacing_from_files(
+                            files[0].frame_positions[0]
+                            , files[0].frame_positions[-1]
+                            , int(len(files[0].frame_positions) / self.num_times)
+                        )
                 else:
                     z_axis = self._z_spacing_from_files(
                         files[0].frame_positions[0]

diff --git a/src/bundles/dicom/src/ui/segmentations.py b/src/bundles/dicom/src/ui/segmentations.py
@@ -709,7 +709,7 @@ def _on_model_removed_from_session(self, *args):
 
     def delete(self):
         self.session.triggers.remove_handler(self.model_added_handler)
-        self.session.triggers.remove_handler(self.model_removed_handler)
+        self.session.triggers.remove_handler(self.model_closed_handler)
         # TODO: Restore old mouse modes if necessary
         if self.session.ui.main_window.view_layout == "orthoplanes":
             self.session.ui.main_window.main_view.clear_segmentation_tool()

diff --git a/src/bundles/list_info/bundle_info.xml b/src/bundles/list_info/bundle_info.xml
@@ -1,4 +1,4 @@
-<BundleInfo name="ChimeraX-ListInfo" version="1.2.1"
+<BundleInfo name="ChimeraX-ListInfo" version="1.2.2"
 	    package="chimerax.list_info"
   	    minSessionVersion="1" maxSessionVersion="1">
 

diff --git a/src/bundles/list_info/src/cmd.py b/src/bundles/list_info/src/cmd.py
@@ -187,13 +187,14 @@ def info_chains(session, atoms=None, attribute="chain_id", *, return_json=False,
         from chimerax.core.commands import atomspec
         atoms = atomspec.everything(session)
     results = atoms.evaluate(session)
-    chains = []
-    for m in results.models:
-        try:
-            chains.extend(m.chains)
-        except AttributeError:
-            # No chains, no problem
-            pass
+    chains = results.atoms.unique_residues.unique_chains
+    #chains = []
+    #for m in results.models:
+    #    try:
+    #        chains.extend(m.chains)
+    #    except AttributeError:
+    #        # No chains, no problem
+    #        pass
     return report_chains(session.logger, chains, attribute, return_json=return_json, save_file=save_file)
 info_chains_desc = CmdDesc(required=[("atoms", Or(AtomSpecArg, EmptyArg))],
                            keyword=[("attribute", StringArg), ('save_file', SaveFileNameArg)],