brukerapi 0.3.0__tar.gz → 0.4.0__tar.gz

{brukerapi-0.3.0/brukerapi.egg-info → brukerapi-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.3.0
+Version: 0.4.0
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
 Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
@@ -16,7 +16,7 @@ Requires-Dist: pyyaml
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: zenodo_get; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: ruff==0.16.0; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Dynamic: license-file
 
@@ -54,6 +54,51 @@ Load any **data set**:
     dataset.data                         # access data array
     dataset.get_value('VisuCoreSize')    # get a parameter value
 
+Raw acquisitions and k-space
+==============================
+
+Raw Bruker acquisitions have format-dependent historical ``.data`` semantics.
+For explicit code, use the representation that matches the task:
+
+.. code-block:: python
+
+    fid = Dataset('{path}/fid')
+    fid.raw                 # decoded (sample, shot, receiver) acquisitions
+    fid.kspace              # ordered FID k-space
+
+    job = Dataset('{path}/rawdata.job0')
+    job.raw                 # decoded (sample, shot, receiver) acquisitions
+    job.kspace              # ordered Cartesian PV360 k-space, when metadata proves the layout
+    job.to_kspace(bart=True)  # optional 16-axis BART layout
+
+``Dataset.data`` remains backward compatible: FIDs expose their historical
+ordered k-space view, whereas PV360 ``rawdata.jobN`` exposes its historical
+decoded stream and emits a ``FutureWarning``. ``.kspace`` is not a
+reconstruction API; EPI and non-Cartesian jobs require acquisition-specific
+handling.
+
+Frame-group metadata
+====================
+
+For 2dseq data, ``frame_group_values`` aligns values named by
+``VisuGroupDepVals`` to the corresponding array axes. Returned arrays use
+singleton dimensions where needed and therefore broadcast directly against
+``dataset.data``:
+
+.. code-block:: python
+
+    echoes = dataset.frame_group_values['VisuAcqEchoTime']
+    b_matrices = dataset.frame_group_values['VisuAcqDiffusionBMatrix']
+
+``metadata`` provides normalized, grouped access to parsed subject, study,
+series, equipment, and acquisition fields:
+
+.. code-block:: python
+
+    dataset.metadata['visu_study']['uid']
+    dataset.metadata['visu_acq']['sequence_name']
+    dataset.metadata['subject']['id']
+
 Load an entire **study**:
 
 .. code-block:: python

{brukerapi-0.3.0 → brukerapi-0.4.0}/README.rst

@@ -32,6 +32,51 @@ Load any **data set**:
     dataset.data                         # access data array
     dataset.get_value('VisuCoreSize')    # get a parameter value
 
+Raw acquisitions and k-space
+==============================
+
+Raw Bruker acquisitions have format-dependent historical ``.data`` semantics.
+For explicit code, use the representation that matches the task:
+
+.. code-block:: python
+
+    fid = Dataset('{path}/fid')
+    fid.raw                 # decoded (sample, shot, receiver) acquisitions
+    fid.kspace              # ordered FID k-space
+
+    job = Dataset('{path}/rawdata.job0')
+    job.raw                 # decoded (sample, shot, receiver) acquisitions
+    job.kspace              # ordered Cartesian PV360 k-space, when metadata proves the layout
+    job.to_kspace(bart=True)  # optional 16-axis BART layout
+
+``Dataset.data`` remains backward compatible: FIDs expose their historical
+ordered k-space view, whereas PV360 ``rawdata.jobN`` exposes its historical
+decoded stream and emits a ``FutureWarning``. ``.kspace`` is not a
+reconstruction API; EPI and non-Cartesian jobs require acquisition-specific
+handling.
+
+Frame-group metadata
+====================
+
+For 2dseq data, ``frame_group_values`` aligns values named by
+``VisuGroupDepVals`` to the corresponding array axes. Returned arrays use
+singleton dimensions where needed and therefore broadcast directly against
+``dataset.data``:
+
+.. code-block:: python
+
+    echoes = dataset.frame_group_values['VisuAcqEchoTime']
+    b_matrices = dataset.frame_group_values['VisuAcqDiffusionBMatrix']
+
+``metadata`` provides normalized, grouped access to parsed subject, study,
+series, equipment, and acquisition fields:
+
+.. code-block:: python
+
+    dataset.metadata['visu_study']['uid']
+    dataset.metadata['visu_acq']['sequence_name']
+    dataset.metadata['subject']['id']
+
 Load an entire **study**:
 
 .. code-block:: python

{brukerapi-0.3.0 → brukerapi-0.4.0}/brukerapi/config/properties_2dseq_core.json

@@ -61,6 +61,14 @@
           ["#VisuCoreWordType",["_8BIT_UNSGN_INT"]],
           ["#VisuCoreByteOrder",["bigEndian"]]
         ]
+    },
+    {
+        "cmd": "np.dtype({'_32BIT_SGN_INT':'int32','_16BIT_SGN_INT':'int16','_32BIT_FLOAT':'float32','_8BIT_UNSGN_INT':'uint8'}[#RECO_wordtype]).newbyteorder('<' if #RECO_byte_order=='littleEndian' else '>')",
+        "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']"]
     }
   ],
   "shape_frames": [
@@ -108,12 +116,24 @@
       {
         "cmd": "#VisuCoreSize.tuple",
         "conditions": []
+      },
+      {
+        "cmd": "#RECO_size.tuple",
+        "conditions": []
+      },
+      {
+        "cmd": "tuple(size for size in (int(#IM_SIX), int(#IM_SIY), int(#IM_SIZ)) if size > 1)",
+        "conditions": []
       }
   ],
   "encoded_dim": [
       {
         "cmd": "len(#VisuCoreSize.tuple)",
         "conditions": []
+      },
+      {
+        "cmd": "len(@shape_block)",
+        "conditions": []
       }
   ],
   "shape_storage":[
@@ -173,7 +193,7 @@
       "conditions": ["@is_single_slice==False"]
     },
     {
-      "cmd": "#VisuCoreDimDesc.list",
+      "cmd": "#VisuCoreDimDesc.list + ['frame']",
       "conditions": ["@is_single_slice==False"]
     }
   ]

{brukerapi-0.3.0 → brukerapi-0.4.0}/brukerapi/config/properties_fid_core.json

@@ -73,48 +73,6 @@
           "#BYTORDA=='big'",
           "#ACQ_sw_version=='<PV-360.1.1>' or #ACQ_sw_version.value.startswith('<PV-360.3.')"
         ]
-    },
-    {
-        "cmd": "np.dtype('i4').newbyteorder('<')",
-        "conditions": [
-          "#DTYPA in [0, 'Integer']",
-          "#BYTORDA=='little'"
-        ]
-    },
-    {
-        "cmd": "np.dtype('i4').newbyteorder('>')",
-        "conditions": [
-          "#DTYPA in [0, 'Integer']",
-          "#BYTORDA=='big'"
-        ]
-    },
-    {
-        "cmd": "np.dtype('f4').newbyteorder('<')",
-        "conditions": [
-          "#DTYPA in [1, 'Float']",
-          "#BYTORDA=='little'"
-        ]
-    },
-    {
-        "cmd": "np.dtype('f4').newbyteorder('>')",
-        "conditions": [
-          "#DTYPA in [1, 'Float']",
-          "#BYTORDA=='big'"
-        ]
-    },
-    {
-        "cmd": "np.dtype('f8').newbyteorder('<')",
-        "conditions": [
-          "#DTYPA in [2, 'Double']",
-          "#BYTORDA=='little'"
-        ]
-    },
-    {
-        "cmd": "np.dtype('f8').newbyteorder('>')",
-        "conditions": [
-          "#DTYPA in [2, 'Double']",
-          "#BYTORDA=='big'"
-        ]
     }
   ],
   "channels": [
@@ -346,6 +304,15 @@
     }
   ],
   "block_count": [
+    {
+      "cmd": "#NPro*#PVM_EncMatrix[2]*#NI*#NR",
+      "conditions": [
+        "@scheme_id=='RADIAL'",
+        "#ACQ_dim==3",
+        "np.atleast_1d(#PVM_EncMatrix).size>2",
+        "#ACQ_size[1]==#NPro*#PVM_EncMatrix[2]"
+      ]
+    },
     {
       "cmd": "#NI*#NR*#PVM_EncMatrix[1]",
       "conditions": [
@@ -428,6 +395,23 @@
     }
   ],
   "encoding_space": [
+    {
+      "cmd": [
+        "#ACQ_size[0]//2",
+        "#PVM_EncNReceivers",
+        "#ACQ_phase_factor",
+        "#NI",
+        "#NPro // #ACQ_phase_factor",
+        "#PVM_EncMatrix[2]",
+        "#NR"
+      ],
+      "conditions": [
+        "@scheme_id=='RADIAL'",
+        "#ACQ_dim==3",
+        "np.atleast_1d(#PVM_EncMatrix).size>2",
+        "#ACQ_size[1]==#NPro*#PVM_EncMatrix[2]"
+      ]
+    },
     {
       "cmd": [
         "#PVM_EncMatrix[0]",
@@ -581,6 +565,15 @@
     }
   ],
   "permute": [
+    {
+      "cmd": [0,2,4,3,5,6,1],
+      "conditions": [
+        "@scheme_id=='RADIAL'",
+        "#ACQ_dim==3",
+        "np.atleast_1d(#PVM_EncMatrix).size>2",
+        "#ACQ_size[1]==#NPro*#PVM_EncMatrix[2]"
+      ]
+    },
     {
       "cmd": [0,2,4,3,5,1],
       "conditions": [
@@ -632,6 +625,22 @@
     }
   ],
   "k_space": [
+    {
+      "cmd": [
+        "#ACQ_size[0]//2",
+        "#NPro",
+        "#PVM_EncMatrix[2]",
+        "#NI",
+        "#NR",
+        "#PVM_EncNReceivers"
+      ],
+      "conditions": [
+        "@scheme_id=='RADIAL'",
+        "#ACQ_dim==3",
+        "np.atleast_1d(#PVM_EncMatrix).size>2",
+        "#ACQ_size[1]==#NPro*#PVM_EncMatrix[2]"
+      ]
+    },
     {
       "cmd": [
         "#PVM_EncMatrix[0]",
@@ -794,7 +803,35 @@
     }
   ],
   "dim_type": [
-        {
+    {
+      "cmd": [
+        "'k_space_encode_step_0'",
+        "'k_space_encode_step_1'",
+        "'k_space_encode_step_2'",
+        "'repetition'",
+        "'channel'"
+      ],
+      "conditions": [
+        "@scheme_id=='RADIAL'",
+        "#ACQ_dim==3",
+        "np.atleast_1d(#PVM_EncMatrix).size>2",
+        "#ACQ_size[1]==#NPro*#PVM_EncMatrix[2]"
+      ]
+    },
+    {
+      "cmd": [
+        "'k_space_encode_step_0'",
+        "'k_space_encode_step_1'",
+        "'slice'",
+        "'repetition'",
+        "'channel'",
+        "'k_space_encode_step_2'"
+      ],
+      "conditions": [
+        "@scheme_id=='dEPI'"
+      ]
+    },
+    {
       "cmd": [
         "'k_space_encode_step_0'",
         "'k_space_encode_step_1'",
@@ -803,7 +840,7 @@
         "'channel'"
       ],
       "conditions": [
-        ["@scheme_id",["CART_2D","RADIAL","EPI","dEPI","SPIRAL","ZTE"]]
+        ["@scheme_id",["CART_2D","RADIAL","EPI","SPIRAL","ZTE"]]
       ]
     },
     {
@@ -821,7 +858,8 @@
     {
       "cmd": [
         "'k_space_encode_step_0'",
-        "'repetition'"
+        "'repetition'",
+        "'average'"
       ],
       "conditions": [
         "@scheme_id=='SPECTROSCOPY'"

{brukerapi-0.3.0 → brukerapi-0.4.0}/brukerapi/config/properties_rawdata_core.json

@@ -76,31 +76,16 @@
     }
   ],
   "job_desc": [
-    {
-      "cmd": "#ACQ_jobs.primed_dict(-1)['<{}>'.format(@subtype)]",
-      "conditions": [
-        ["#ACQ_sw_version",["<PV-360.1.1>"]]
-      ]
-    },
     {
       "cmd": "[v for v in #ACQ_jobs.nested if v[-1] == '<{}>'.format(@subtype)][0]",
       "conditions": [
-        "#ACQ_sw_version.value.startswith('<PV-360.3.')"
-      ]
-    },
-
-    {
-      "cmd": "#ACQ_jobs.nested[0]",
-      "conditions": [
-        "#ACQ_sw_version in ['<PV 5.1>', '<PV 6.0>', '<PV 6.0.1>', '<PV-7.0.0>']",
-        "@subtype == 'job0'"
+        "len(#ACQ_jobs.nested[0])==9"
       ]
     },
     {
-      "cmd": "#ACQ_jobs.nested[1]",
+      "cmd": "#ACQ_jobs.nested[int(@subtype[3:])]",
       "conditions": [
-        "#ACQ_sw_version in ['<PV 5.1>', '<PV 6.0>', '<PV 6.0.1>', '<PV-7.0.0>']",
-        "@subtype == 'job1'"
+        "len(#ACQ_jobs.nested[0])==8"
       ]
     }
   ],
@@ -111,15 +96,15 @@
       ]
     }
   ],
-  "shape_storage": [
+  "dim_type": [
     {
-      "cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[6],)",
-      "conditions": [
-        "#ACQ_sw_version.value.startswith('<PV-360.3.')"
-      ]
-    },
+      "cmd": ["'sample'", "'channel'", "'scan'"],
+      "conditions": []
+    }
+  ],
+  "shape_storage": [
     {
-      "cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[3],)",
+      "cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[6] if len(@job_desc)==9 else @job_desc[3],)",
       "conditions": []
     }
   ]

{brukerapi-0.3.0 → brukerapi-0.4.0}/brukerapi/config/properties_traj_core.json

@@ -68,6 +68,12 @@
       ]
     }
   ],
+  "dim_type": [
+    {
+      "cmd": ["'axis'", "'sample'", "'projection'"],
+      "conditions": []
+    }
+  ],
   "shape_storage": [
     {
       "cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro), #NPro)",

brukerapi-0.4.0/brukerapi/config/properties_traj_custom.json

@@ -0,0 +1,38 @@
+{
+  "subj_id": [
+    {
+      "cmd": "#SUBJECT_id[1:-1]",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "study_id": [
+    {
+      "cmd": "str(#SUBJECT_study_nr)",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "exp_id": [
+    {
+      "cmd": "@path.parent.name",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "id": [
+    {
+      "cmd": "'Traj_{}*{}*{}'.format(@exp_id, @subj_id, @study_id)",
+      "conditions": []
+    }
+  ]
+}