Close the spec paths the corpus never exercises (D3, D5-D8, R3, R8, J8)

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
+        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(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/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": "tuple(size for size in (int(#IM_SIX), int(#IM_SIY), int(#IM_SIZ)) if size > 1)",
+        "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": "#RECO_size.tuple",
         "conditions": []
       }
   ],
@@ -165,8 +176,9 @@
       "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 +193,11 @@
   ],
   "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/config/properties_2dseq_custom.json

@@ -58,15 +58,15 @@
     {
       "cmd": "np.array([#PVM_VoxArrSize[0,0] * #VisuAcqSize[1], #PVM_VoxArrSize[0,1] * #VisuAcqSize[2], #VisuCoreFrameThickness])",
       "conditions": [
-        "#VisuCreatorVersion in ['<5.1>']",
+        "@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": [
-        "#VisuCreatorVersion in ['<6.0.1>']",
+        "@pv_version.split('.')[0]!='5'",
         "#VisuCoreDimDesc.list[0]=='spectroscopic'",
         "#VisuCoreDimDesc.list[1]=='spatial'",
         "#VisuCoreDimDesc.list[2]=='spatial'"]
@@ -97,49 +97,34 @@
     {
       "cmd": "np.array([#PVM_VoxArrSize[0,0], #PVM_VoxArrSize[0,1], #VisuCoreFrameThickness])",
       "conditions": [
-        "#VisuCreatorVersion in ['<5.1>']",
+        "@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": [
-        "#VisuCreatorVersion in ['<6.0.1>']",
+        "@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], #VisuCoreFrameThickness + #VisuCoreSlicePacksSliceDist.list[0]])",
-      "conditions": [
-        "#VisuCreatorVersion in ['<6.0.1>']",
-        "#VisuCoreDim==2"]
-    },
-    {
-      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], abs(#VisuCorePosition[0,2] - #VisuCorePosition[1,2])])",
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], np.linalg.norm(#VisuCorePosition[1,:] - #VisuCorePosition[0,:])])",
       "conditions": [
-        "#VisuCreatorVersion in ['<5.1>']",
         "#VisuCorePosition.size[0]>1",
-        "#VisuCoreDim==2"]
+        "#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], #VisuCoreFrameThickness])",
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreSlicePacksSliceDist.list[0]])",
       "conditions": [
-        "#VisuCreatorVersion in ['<5.1>']",
-        "#VisuCorePosition.size[0]==1",
-        "#VisuCoreDim==2"]
-    },
-    {
-      "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"]
     },
     {
       "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreFrameThickness])",
       "conditions": [
-        "#VisuCorePosition.size[0]==1",
         "#VisuCoreDim==2"]
     },
     {
@@ -150,96 +135,6 @@
         "#VisuCoreDimDesc.list[2]=='spatial'"]
     }
   ],
-  "position_matrix": [
-      {
-        "cmd": "np.array([[np.cos(np.pi), -np.sin(np.pi), 0], [np.sin(np.pi), np.cos(np.pi), 0], [0, 0, 1]])",
-        "conditions": [
-          "#VisuSubjectPosition=='Head_Supine'"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])",
-        "conditions": [
-          "#VisuSubjectPosition=='Head_Prone'"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[np.cos(np.pi/2), -np.sin(np.pi/2), 0], [np.sin(np.pi/2), np.cos(np.pi/2), 0], [0, 0, 1]])",
-        "conditions": [
-          "#VisuSubjectPosition=='Head_Left'"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[np.cos(-np.pi/2), -np.sin(-np.pi/2), 0], [np.sin(-np.pi/2), np.cos(-np.pi/2), 0], [0, 0, 1]])",
-        "conditions": [
-          "#VisuSubjectPosition=='Head_Right'"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[1, 0, 0], [0, np.cos(np.pi), -np.sin(np.pi)], [0, np.sin(np.pi), np.cos(np.pi)]]).astype('float')",
-        "conditions": [
-          "#VisuSubjectPosition in ['Foot_Supine', 'Tail_Supine']"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[np.cos(np.pi), 0, np.sin(np.pi)], [0, 1, 0], [-np.sin(np.pi), 0, np.cos(np.pi)]]).astype('float')",
-        "conditions": [
-          "#VisuSubjectPosition in ['Foot_Prone', 'Tail_Prone']"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[np.cos(np.pi/2), -np.sin(np.pi/2), 0], [np.sin(np.pi/2), np.cos(np.pi/2), 0], [0, 0, 1]])",
-        "conditions": [
-          "#VisuSubjectPosition in ['Foot_Left', 'Tail_Left']"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      },
-      {
-        "cmd": "np.array([[np.cos(-np.pi/2), -np.sin(-np.pi/2), 0], [np.sin(-np.pi/2), np.cos(-np.pi/2), 0], [0, 0, 1]])",
-        "conditions": [
-          "#VisuSubjectPosition in ['Foot_Right', 'Tail_Right']"
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      }
-  ],
-  "rotation": [
-      {
-        "cmd": "np.dot(@position_matrix, np.reshape(#VisuCoreOrientation[0,:],(3,3)).T.dot(np.diag(@resolution)))",
-        "conditions": [
-        ],
-        "reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
-      }
-  ],
-  "position": [
-    {
-      "cmd": "#PVM_VoxArrPosition[0,:].astype(np.float64)",
-      "conditions": [
-        "#VisuCoreDimDesc.list[0]=='spectroscopic'",
-        "#VisuCoreDimDesc.list[1]=='spatial'",
-        "#VisuCoreDimDesc.list[2]=='spatial'"]
-    },
-    {
-      "cmd": "np.array([#VisuCorePosition[0,0] + @extent[0], #VisuCorePosition[0,1] + @extent[1], #VisuCorePosition[0,2]])",
-      "conditions": []
-    }
-  ],
-  "affine": [
-      {
-        "cmd": "np.array([[@rotation[0,0], @rotation[0,1], @rotation[0,2], @position[0]],[@rotation[1,0], @rotation[1,1], @rotation[1,2], @position[1]],[@rotation[2,0], @rotation[2,1], @rotation[2,2], @position[2]],[0, 0, 0, 1]])",
-        "conditions": []
-      },
-      {
-        "cmd": "np.identity(4)",
-        "conditions": [],
-        "comment": "default value"
-      }
-  ],
   "TE": [
       {
         "cmd": "#VisuAcqEchoTime",