brukerapi 0.4.1__tar.gz → 0.4.2__tar.gz

{brukerapi-0.4.1/brukerapi.egg-info → brukerapi-0.4.2}/PKG-INFO

@@ -1,23 +1,23 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.4.1
+Version: 0.4.2
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
 Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
 License: MIT
 Project-URL: Homepage, https://github.com/isi-nmr/brukerapi-python
 Project-URL: Download, https://github.com/isi-nmr/brukerapi-python/releases/latest
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: numpy<2; python_version < "3.9"
-Requires-Dist: numpy>=1.26.0; python_version >= "3.9"
+Requires-Dist: numpy>=2.1; python_version >= "3.10"
 Requires-Dist: pyyaml
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: zenodo_get; extra == "dev"
 Requires-Dist: ruff==0.16.0; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pyrefly; extra == "dev"
 Dynamic: license-file
 
 brukerapi-python

brukerapi-0.4.2/brukerapi/__init__.py

@@ -0,0 +1 @@
+__all__ = ["dataset", "exceptions", "folders", "jcampdx", "utils"]

{brukerapi-0.4.1 → brukerapi-0.4.2}/brukerapi/cli.py

@@ -112,9 +112,9 @@ def split(args):
     dataset = Dataset(args.path_in)
 
     if args.slice_package:
-        SlicePackageSplitter().split(dataset, write=True)
+        SlicePackageSplitter().split(dataset, write=True, path_out=args.path_out)
     elif args.frame_group:
-        FrameGroupSplitter(args.frame_group).split(dataset, write=True)
+        FrameGroupSplitter(args.frame_group).split(dataset, write=True, path_out=args.path_out)
 
 
 def report(args):
@@ -124,25 +124,25 @@ def report(args):
     :return:
     """
     input = Path(args.input)
-
-    if args.output is None:
-        output = None
-    else:
-        output = Path(args.output)
+    output = None if args.output is None else Path(args.output)
 
     if input.is_dir():
         # folder in-place
         if output is None:
-            Folder(input).report(format_=args.format, props=args.props, verbose=args.verbose)
-        elif output.is_dir():
-            # folder to folder
-            Folder(input).report(path_out=output, format_=args.format, props=args.props, verbose=args.verbose)
+            Folder(str(input)).report(format_=args.format, props=args.props, verbose=args.verbose)
+        else:
+            # folder to folder -- an output folder that does not exist yet is
+            # created rather than silently matching no branch and exiting 0
+            output.mkdir(parents=True, exist_ok=True)
+            Folder(str(input)).report(path_out=output, format_=args.format, props=args.props, verbose=args.verbose)
     # dataset in-place
     elif output is None:
-        Dataset(input, add_parameters=["subject"]).report(props=args.props, verbose=args.verbose)
+        Dataset(input, add_parameters=["subject"]).report(props=args.props, verbose=args.verbose, format_=args.format)
     # dataset to folder, or dataset to file
     else:
-        Dataset(input, add_parameters=["subject"]).report(path=output, props=args.props, verbose=args.verbose)
+        if not output.suffix:
+            output.mkdir(parents=True, exist_ok=True)
+        Dataset(input, add_parameters=["subject"]).report(path=output, props=args.props, verbose=args.verbose, format_=args.format)
 
 
 def filter(args):

{brukerapi-0.4.1 → brukerapi-0.4.2}/brukerapi/config/properties_2dseq_core.json

@@ -1,8 +1,9 @@
 {
   "pv_version": [
       {
-        "cmd": "#VisuCreatorVersion[1:-1]",
-        "conditions": []
+        "cmd": "#VisuCreatorVersion[1:-1].split(';')[0]",
+        "conditions": [],
+        "comment": "spec 7.1: VisuCreator/VisuCreatorVersion are semicolon-separated lists; the first creator is the one that wrote the dataset"
       }
   ],
   "numpy_dtype": [
@@ -67,8 +68,12 @@
         "conditions": ["#RECO_wordtype in ['_32BIT_SGN_INT','_16BIT_SGN_INT','_32BIT_FLOAT','_8BIT_UNSGN_INT']", "#RECO_byte_order in ['littleEndian','bigEndian']"]
     },
     {
-        "cmd": "np.dtype({'ip_int':'int32','ip_short':'int16','ip_float':'float32'}[#DATTYPE]).newbyteorder('<')",
-        "conditions": ["#DATTYPE in ['ip_int','ip_short','ip_float']"]
+        "cmd": "np.dtype(DATTYPE_WORD_TYPES[str(#DATTYPE)]).newbyteorder('>' if int(np.atleast_1d(#PR_STA)[15]) else '<')",
+        "conditions": ["str(#DATTYPE) in DATTYPE_WORD_TYPES", "len(np.atleast_1d(#PR_STA))>15"]
+    },
+    {
+        "cmd": "np.dtype(DATTYPE_WORD_TYPES[str(#DATTYPE)]).newbyteorder('<')",
+        "conditions": ["str(#DATTYPE) in DATTYPE_WORD_TYPES"]
     }
   ],
   "shape_frames": [
@@ -118,11 +123,17 @@
         "conditions": []
       },
       {
-        "cmd": "#RECO_size.tuple",
-        "conditions": []
+        "cmd": "(int(#IM_SIX), int(#IM_SIY))",
+        "conditions": [],
+        "comment": "spec 8: IM_SIX/IM_SIY are the in-plane matrix written after transposition; IM_SIZ is the number of frames, which shape_frames already counts"
+      },
+      {
+        "cmd": "transposed_size(#RECO_size.tuple, #RECO_transposition)",
+        "conditions": [],
+        "comment": "spec 6.9: RECO_size still refers to the non-transposed ordering, so the stored frame shape is RECO_size with the recorded exchange applied"
       },
       {
-        "cmd": "tuple(size for size in (int(#IM_SIX), int(#IM_SIY), int(#IM_SIZ)) if size > 1)",
+        "cmd": "#RECO_size.tuple",
         "conditions": []
       }
   ],
@@ -150,14 +161,9 @@
   ],
   "num_slice_packages": [
       {
-        "cmd": "len(#VisuCoreSlicePacksSlices.nested)",
-        "conditions": []
-      },
-      {
-        "cmd": "1",
+        "cmd": "len(@slice_packages_index())",
         "conditions": []
       }
-
   ],
   "slope": [
     {
@@ -165,8 +171,9 @@
       "conditions": []
     },
     {
-      "cmd": "#RECO_map_slope.array",
-      "conditions": []
+      "cmd": "1.0 / #RECO_map_slope.array",
+      "conditions": [],
+      "comment": "spec 3.4: real = pixel / RECO_map_slope + RECO_map_offset, so VisuCoreDataSlope = 1 / RECO_map_slope. Multiplying instead of dividing makes values slope^2 too small"
     }
   ],
   "offset": [
@@ -181,11 +188,11 @@
   ],
   "dim_type": [
     {
-      "cmd": "#VisuCoreDimDesc.list + ['spatial',] + #VisuFGOrderDesc.sub_list(1)",
+      "cmd": "#VisuCoreDimDesc.list + ['frame',] + #VisuFGOrderDesc.sub_list(1)",
       "conditions": ["@is_single_slice==True"]
     },
     {
-      "cmd": "#VisuCoreDimDesc.list + ['spatial',]",
+      "cmd": "#VisuCoreDimDesc.list + ['frame',]",
       "conditions": ["@is_single_slice==True"]
     },
     {

brukerapi-0.4.2/brukerapi/config/properties_2dseq_custom.json

@@ -0,0 +1,184 @@
+{
+  "subj_id": [
+      {
+        "cmd": "#VisuSubjectName[1:-1]",
+        "conditions": [
+        ]
+      },
+      {
+        "cmd": "''",
+        "conditions": [
+        ]
+      }
+  ],
+  "study_id": [
+      {
+        "cmd": "str(#VisuStudyNumber)",
+        "conditions": [
+        ]
+      },
+      {
+        "cmd": "''",
+        "conditions": [
+        ]
+      }
+  ],
+  "exp_id": [
+      {
+        "cmd": "@path.parents[2].name",
+        "conditions": [
+        ]
+      },
+      {
+        "cmd": "''",
+        "conditions": [
+        ]
+      }
+  ],
+  "proc_id": [
+      {
+        "cmd": "@path.parents[0].name",
+        "conditions": [
+        ]
+      },
+      {
+        "cmd": "''",
+        "conditions": [
+        ]
+      }
+  ],
+  "id": [
+      {
+        "cmd": "'2DSEQ_{}_{}_{}_{}'.format(@exp_id, @proc_id, @subj_id, @study_id)",
+        "conditions": [
+        ]
+      }
+  ],
+  "extent": [
+    {
+      "cmd": "np.array([#PVM_VoxArrSize[0,0] * #VisuAcqSize[1], #PVM_VoxArrSize[0,1] * #VisuAcqSize[2], #VisuCoreFrameThickness])",
+      "conditions": [
+        "@pv_version.split('.')[0]=='5'",
+        "#VisuCoreDimDesc.list[0]=='spectroscopic'",
+        "#VisuCoreDimDesc.list[1]=='spatial'",
+        "#VisuCoreDimDesc.list[2]=='spatial'"]
+    },
+    {
+      "cmd": "np.array([#PVM_VoxArrSize[0,0], #PVM_VoxArrSize[0,1], #PVM_VoxArrSize[0,2]])",
+      "conditions": [
+        "@pv_version.split('.')[0]!='5'",
+        "#VisuCoreDimDesc.list[0]=='spectroscopic'",
+        "#VisuCoreDimDesc.list[1]=='spatial'",
+        "#VisuCoreDimDesc.list[2]=='spatial'"]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0], #VisuCoreExtent[1], (np.shape(#VisuCorePosition)[0] + 1 ) * abs(#VisuCorePosition[1,2] - #VisuCorePosition[0,2])])",
+      "conditions": [
+        "#VisuCorePosition.size[0]>1",
+        "#VisuCoreDim==2"
+      ]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0], #VisuCoreExtent[1], #VisuCoreFrameThickness])",
+      "conditions": [
+        "#VisuCorePosition.size[0]==1",
+        "#VisuCoreDim==2"
+      ]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0], #VisuCoreExtent[1], #VisuCoreExtent[2]])",
+      "conditions": [
+        "#VisuCoreDimDesc.list[0]=='spatial'",
+        "#VisuCoreDimDesc.list[1]=='spatial'",
+        "#VisuCoreDimDesc.list[2]=='spatial'"]
+    }
+  ],
+  "resolution": [
+    {
+      "cmd": "np.array([#PVM_VoxArrSize[0,0], #PVM_VoxArrSize[0,1], #VisuCoreFrameThickness])",
+      "conditions": [
+        "@pv_version.split('.')[0]=='5'",
+        "#VisuCoreDimDesc.list[0]=='spectroscopic'",
+        "#VisuCoreDimDesc.list[1]=='spatial'",
+        "#VisuCoreDimDesc.list[2]=='spatial'"]
+    },
+    {
+      "cmd": "np.array([#PVM_VoxArrSize[0,0] / #VisuCoreSize[1], #PVM_VoxArrSize[0,1] / #VisuCoreSize[2], #PVM_VoxArrSize[0,2]])",
+      "conditions": [
+        "@pv_version.split('.')[0]!='5'",
+        "#VisuCoreDimDesc.list[0]=='spectroscopic'",
+        "#VisuCoreDimDesc.list[1]=='spatial'",
+        "#VisuCoreDimDesc.list[2]=='spatial'"]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], np.linalg.norm(#VisuCorePosition[1,:] - #VisuCorePosition[0,:])])",
+      "conditions": [
+        "#VisuCorePosition.size[0]>1",
+        "#VisuCoreDim==2"],
+      "comment": "spec 7.10: the distance between two measured slice centres. VisuCoreSlicePacksSliceDist is already centre-to-centre, so it must not be added to VisuCoreFrameThickness"
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreSlicePacksSliceDist.list[0]])",
+      "conditions": [
+        "#VisuCoreDim==2"]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreFrameThickness])",
+      "conditions": [
+        "#VisuCoreDim==2"]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreExtent[2] / #VisuCoreSize[2]])",
+      "conditions": [
+        "#VisuCoreDimDesc.list[0]=='spatial'",
+        "#VisuCoreDimDesc.list[1]=='spatial'",
+        "#VisuCoreDimDesc.list[2]=='spatial'"]
+    }
+  ],
+  "TE": [
+      {
+        "cmd": "#VisuAcqEchoTime",
+        "conditions": [
+        ]
+      }
+  ],
+  "TR": [
+      {
+        "cmd": "#VisuAcqRepetitionTime",
+        "conditions": [
+        ]
+      }
+  ],
+  "imaging_frequency": [
+    {
+        "cmd": "#VisuAcqImagingFrequency",
+        "conditions": [
+        ]
+    }
+  ],
+  "date": [
+      {
+        "cmd": "datetime.datetime.strptime(#VisuStudyDate[1:-1], '%X %d %b %Y')",
+        "conditions": [
+          "'T' not in #VisuStudyDate"
+        ]
+      },
+      {
+        "cmd": "datetime.datetime.strptime(#VisuStudyDate[1:-1], '%Y-%m-%dT%X,%f%z')",
+        "conditions": [
+          "'T' in #VisuStudyDate"
+        ]
+      }
+  ],
+  "dwell_s": [
+    {
+      "cmd": "1./ (#VisuAcqPixelBandwidth * #VisuCoreSize.list[0])  / 2.",
+      "conditions": []
+    },
+    {
+      "cmd": "None",
+      "conditions": [],
+      "comment": "default value"
+    }
+  ]
+}