brukerapi 0.2.5__tar.gz → 0.3.0__tar.gz

{brukerapi-0.2.5/brukerapi.egg-info → brukerapi-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.2.5
+Version: 0.3.0
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
 Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
@@ -50,9 +50,9 @@ Load any **data set**:
 .. code-block:: python
 
     from brukerapi.dataset import Dataset
-    dataset = Dataset('{path}/2dseq')    # create data set, works for fid, 2dseq, rawdata.x, ser
+    dataset = Dataset('{path}/2dseq')    # also supports fid, fid_proc.64, traj, and rawdata.jobN
     dataset.data                         # access data array
-    dataset.VisuCoreSize                 # get a value of a single parameter
+    dataset.get_value('VisuCoreSize')    # get a parameter value
 
 Load an entire **study**:
 
@@ -62,17 +62,7 @@ Load an entire **study**:
     study = Study('{path_to_study_folder}')
     dataset = study.get_dataset(exp_id='1', proc_id='1')
 
-    # get_dataset returns an empty dataset
-    # in order to load data into the data set, you can either use the context manager:
-
-    with dataset as d:
-        d.data                         # access data array
-        d.VisuCoreSize                 # get a value of a parameter
-
-    # or the load function
-    dataset.load()
-    dataset.data                       # access data array
-    dataset.VisuCoreSize               # get a value of a single parameter
+    dataset.data                         # Study loads datasets by default
 
 Load a parametric file:
 
@@ -82,8 +72,8 @@ Load a parametric file:
 
    parameters = JCAMPDX('path_to_scan/method')
    
-   TR = data.params["PVM_RepetitionTime"].value # This way
-   TR = data.get_value("PVM_RepetitionTime") # Or this way
+   TR = parameters.params["PVM_RepetitionTime"].value
+   TR = parameters.get_value("PVM_RepetitionTime")
 
 
 
@@ -94,16 +84,17 @@ Features
 
 * **I/O** interface for **fid** data sets
 * **I/O** interface for **2dseq** data sets
-* **I/O** interface for **ser** data sets
 * **I/O** interface for **rawdata** data sets
 * **Random access** for **fid** and **2dseq** data sets
 * **Split** operation implemented over **2dseq** data sets
 * **Filter** operation implemented over Bruker **folders** (allowing you to work with a subset of your study only)
+* ParaVision 5.1, 6.0.1, 7.0.0, and 360 metadata and binary-layout support
+* Metadata-based fallback inference for custom Cartesian, EPI, radial/UTE, spiral, ZTE, CSI, and spectroscopy sequences
 
 Examples
 ========
 
-* How to `read <examples/read_fid.ipynb>`_ a Bruker fid, 2dseq, rawdata, or ser file
+* How to `read <examples/read_fid.ipynb>`_ a Bruker fid, 2dseq, or rawdata file
 * How to `split slice packages <examples/split_sp_demo.ipynb>`_ of a 2dseq data set
 * How to `split FG_ECHO <examples/split_fg_echo_demo.ipynb>`_ of a 2dseq data set
 * How to `split FG_ISA <examples/examples/split_fg_isa_demo.ipynb>`_ of a 2dseq data set
@@ -128,8 +119,7 @@ From source:
 
     git clone https://github.com/isi-nmr/brukerapi-python.git
     cd brukerapi-python
-    python setup.py build
-    python setup.py install
+    python -m pip install -e .[dev]
 
 Testing
 ========
@@ -138,108 +128,38 @@ data sets:
 
 * `BrukerAPI test data set (Bruker ParaVision v5.1) <https://doi.org/10.5281/zenodo.3899268>`_
 * `BrukerAPI test data set (Bruker ParaVision v6.0.1) <https://doi.org/10.5281/zenodo.3894651>`_
-* `bruker2nifti_qa data set <https://gitlab.com/naveau/bruker2nifti_qa>`_
+* BrukerAPI test data set for ParaVision v7.0.0 (Zenodo DOI collection ``10.5281/zenodo.4522220``)
+* `PV360 standard data <https://github.com/cecilyen/PV360_StdData>`_
+
+The corpus download is opt-in for local runs:
+
+.. code-block:: shell
+
+    python -m pytest test --download_test_data
+
+Without that flag, pytest uses any corpus already present under ``test/test_data`` and
+skips unavailable collections.
+
+File format reference
+=====================
+
+`Bruker ParaVision Raw Data Format
+<https://github.com/gdevenyi/brkraw-legacy/blob/main/FILE_FORMAT.md>`_ is the source of truth
+for file-format parsing, binary layouts, dataset typing, and metadata-driven acquisition
+scheme inference in this project.
 
 Compatibility
 =============
 
-The API was tested using various data sets obtained by **ParaVision 5.1**, **6.0.1** and **360**. It it is compatible
-with the following data set types from individual ParaVision versions.
-
-ParaVision v5.1
-"""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* NSPECT.ppg
-* PRESS.ppg
-* STEAM.ppg
-* igFLASH.ppg
-
-ParaVision v6.0.1 and v7.0.0
-"""""""""""""""""""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg,
-* FLASHAngio.ppg
-* IgFLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* CASL_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* SINGLEPULSE.ppg
-* NSPECT.ppg
-* EPSI.ppg
-* PRESS.ppg
-* STEAM.ppg
-* ISIS.ppg
-* CPMG.ppg
-* RfProfile.ppg
-
-
-ParaVision 360 v1.1 v3.0-v3.7
-"""""""""""""""""""""""""""""""""
-Reading rawdata is supported only in a basic form, no reshaping into k-space is supported at the moment.
-Compatible data set types:
-
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
+Tested releases are ParaVision 5.1, 6.0.1, 7.0.0, and PV360 3.x. Supported
+primary binaries are ``fid``, ``fid_proc.64``, ``2dseq``, ``traj``,
+``rawdata.jobN``, and ``rawdata.Navigator``. Known ``fid.spiral``,
+``fid.navFid``, and ``fid.orig`` files are exposed as auxiliary subdatasets of
+their parent ``fid``; they are not accepted as standalone primary datasets.
+TopSpin/NMR ``ser`` is intentionally unsupported.
+
+Known pulse-program names use dedicated layouts. For custom sequences the
+reader also infers common acquisition families from metadata; callers can pass
+``scheme_id=`` when inference is ambiguous. Rawdata is returned as complex
+ordered samples, not as reconstructed k-space. See the compatibility page in
+the documentation for behavior and current reconstruction limitations.

{brukerapi-0.2.5 → brukerapi-0.3.0}/README.rst

@@ -28,9 +28,9 @@ Load any **data set**:
 .. code-block:: python
 
     from brukerapi.dataset import Dataset
-    dataset = Dataset('{path}/2dseq')    # create data set, works for fid, 2dseq, rawdata.x, ser
+    dataset = Dataset('{path}/2dseq')    # also supports fid, fid_proc.64, traj, and rawdata.jobN
     dataset.data                         # access data array
-    dataset.VisuCoreSize                 # get a value of a single parameter
+    dataset.get_value('VisuCoreSize')    # get a parameter value
 
 Load an entire **study**:
 
@@ -40,17 +40,7 @@ Load an entire **study**:
     study = Study('{path_to_study_folder}')
     dataset = study.get_dataset(exp_id='1', proc_id='1')
 
-    # get_dataset returns an empty dataset
-    # in order to load data into the data set, you can either use the context manager:
-
-    with dataset as d:
-        d.data                         # access data array
-        d.VisuCoreSize                 # get a value of a parameter
-
-    # or the load function
-    dataset.load()
-    dataset.data                       # access data array
-    dataset.VisuCoreSize               # get a value of a single parameter
+    dataset.data                         # Study loads datasets by default
 
 Load a parametric file:
 
@@ -60,8 +50,8 @@ Load a parametric file:
 
    parameters = JCAMPDX('path_to_scan/method')
    
-   TR = data.params["PVM_RepetitionTime"].value # This way
-   TR = data.get_value("PVM_RepetitionTime") # Or this way
+   TR = parameters.params["PVM_RepetitionTime"].value
+   TR = parameters.get_value("PVM_RepetitionTime")
 
 
 
@@ -72,16 +62,17 @@ Features
 
 * **I/O** interface for **fid** data sets
 * **I/O** interface for **2dseq** data sets
-* **I/O** interface for **ser** data sets
 * **I/O** interface for **rawdata** data sets
 * **Random access** for **fid** and **2dseq** data sets
 * **Split** operation implemented over **2dseq** data sets
 * **Filter** operation implemented over Bruker **folders** (allowing you to work with a subset of your study only)
+* ParaVision 5.1, 6.0.1, 7.0.0, and 360 metadata and binary-layout support
+* Metadata-based fallback inference for custom Cartesian, EPI, radial/UTE, spiral, ZTE, CSI, and spectroscopy sequences
 
 Examples
 ========
 
-* How to `read <examples/read_fid.ipynb>`_ a Bruker fid, 2dseq, rawdata, or ser file
+* How to `read <examples/read_fid.ipynb>`_ a Bruker fid, 2dseq, or rawdata file
 * How to `split slice packages <examples/split_sp_demo.ipynb>`_ of a 2dseq data set
 * How to `split FG_ECHO <examples/split_fg_echo_demo.ipynb>`_ of a 2dseq data set
 * How to `split FG_ISA <examples/examples/split_fg_isa_demo.ipynb>`_ of a 2dseq data set
@@ -106,8 +97,7 @@ From source:
 
     git clone https://github.com/isi-nmr/brukerapi-python.git
     cd brukerapi-python
-    python setup.py build
-    python setup.py install
+    python -m pip install -e .[dev]
 
 Testing
 ========
@@ -116,108 +106,38 @@ data sets:
 
 * `BrukerAPI test data set (Bruker ParaVision v5.1) <https://doi.org/10.5281/zenodo.3899268>`_
 * `BrukerAPI test data set (Bruker ParaVision v6.0.1) <https://doi.org/10.5281/zenodo.3894651>`_
-* `bruker2nifti_qa data set <https://gitlab.com/naveau/bruker2nifti_qa>`_
+* BrukerAPI test data set for ParaVision v7.0.0 (Zenodo DOI collection ``10.5281/zenodo.4522220``)
+* `PV360 standard data <https://github.com/cecilyen/PV360_StdData>`_
+
+The corpus download is opt-in for local runs:
+
+.. code-block:: shell
+
+    python -m pytest test --download_test_data
+
+Without that flag, pytest uses any corpus already present under ``test/test_data`` and
+skips unavailable collections.
+
+File format reference
+=====================
+
+`Bruker ParaVision Raw Data Format
+<https://github.com/gdevenyi/brkraw-legacy/blob/main/FILE_FORMAT.md>`_ is the source of truth
+for file-format parsing, binary layouts, dataset typing, and metadata-driven acquisition
+scheme inference in this project.
 
 Compatibility
 =============
 
-The API was tested using various data sets obtained by **ParaVision 5.1**, **6.0.1** and **360**. It it is compatible
-with the following data set types from individual ParaVision versions.
-
-ParaVision v5.1
-"""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* NSPECT.ppg
-* PRESS.ppg
-* STEAM.ppg
-* igFLASH.ppg
-
-ParaVision v6.0.1 and v7.0.0
-"""""""""""""""""""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg,
-* FLASHAngio.ppg
-* IgFLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* CASL_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* SINGLEPULSE.ppg
-* NSPECT.ppg
-* EPSI.ppg
-* PRESS.ppg
-* STEAM.ppg
-* ISIS.ppg
-* CPMG.ppg
-* RfProfile.ppg
-
-
-ParaVision 360 v1.1 v3.0-v3.7
-"""""""""""""""""""""""""""""""""
-Reading rawdata is supported only in a basic form, no reshaping into k-space is supported at the moment.
-Compatible data set types:
-
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
+Tested releases are ParaVision 5.1, 6.0.1, 7.0.0, and PV360 3.x. Supported
+primary binaries are ``fid``, ``fid_proc.64``, ``2dseq``, ``traj``,
+``rawdata.jobN``, and ``rawdata.Navigator``. Known ``fid.spiral``,
+``fid.navFid``, and ``fid.orig`` files are exposed as auxiliary subdatasets of
+their parent ``fid``; they are not accepted as standalone primary datasets.
+TopSpin/NMR ``ser`` is intentionally unsupported.
+
+Known pulse-program names use dedicated layouts. For custom sequences the
+reader also infers common acquisition families from metadata; callers can pass
+``scheme_id=`` when inference is ambiguous. Rawdata is returned as complex
+ordered samples, not as reconstructed k-space. See the compatibility page in
+the documentation for behavior and current reconstruction limitations.

{brukerapi-0.2.5 → brukerapi-0.3.0}/brukerapi/cli.py

@@ -141,7 +141,7 @@ def report(args):
     elif output is None:
         Dataset(input, add_parameters=["subject"]).report(props=args.props, verbose=args.verbose)
     # dataset to folder, or dataset to file
-    elif output.is_dir():
+    else:
         Dataset(input, add_parameters=["subject"]).report(path=output, props=args.props, verbose=args.verbose)
 
 

{brukerapi-0.2.5 → brukerapi-0.3.0}/brukerapi/config/properties_2dseq_core.json

@@ -30,7 +30,7 @@
     {
         "cmd": "np.dtype('uint8').newbyteorder('<')",
         "conditions": [
-          ["#VisuCoreWordType",["_8BIT_USGN_INT"]],
+          ["#VisuCoreWordType",["_8BIT_UNSGN_INT"]],
           ["#VisuCoreByteOrder",["littleEndian"]]
         ]
     },
@@ -58,7 +58,7 @@
     {
         "cmd": "np.dtype('uint8').newbyteorder('>')",
         "conditions": [
-          ["#VisuCoreWordType",["_8BIT_USGN_INT"]],
+          ["#VisuCoreWordType",["_8BIT_UNSGN_INT"]],
           ["#VisuCoreByteOrder",["bigEndian"]]
         ]
     }
@@ -143,12 +143,20 @@
     {
       "cmd": "#VisuCoreDataSlope.array",
       "conditions": []
+    },
+    {
+      "cmd": "#RECO_map_slope.array",
+      "conditions": []
     }
   ],
   "offset": [
     {
       "cmd": "#VisuCoreDataOffs.array",
       "conditions": []
+    },
+    {
+      "cmd": "#RECO_map_offset.array",
+      "conditions": []
     }
   ],
   "dim_type": [
@@ -169,4 +177,4 @@
       "conditions": ["@is_single_slice==False"]
     }
   ]
-}
+}

{brukerapi-0.2.5 → brukerapi-0.3.0}/brukerapi/config/properties_2dseq_custom.json

@@ -130,6 +130,18 @@
         "#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"]
+    },
     {
       "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreExtent[2] / #VisuCoreSize[2]])",
       "conditions": [
@@ -253,13 +265,13 @@
       {
         "cmd": "datetime.datetime.strptime(#VisuStudyDate[1:-1], '%X %d %b %Y')",
         "conditions": [
-          "#VisuVersion==1"
+          "'T' not in #VisuStudyDate"
         ]
       },
       {
         "cmd": "datetime.datetime.strptime(#VisuStudyDate[1:-1], '%Y-%m-%dT%X,%f%z')",
         "conditions": [
-          "#VisuVersion==3"
+          "'T' in #VisuStudyDate"
         ]
       }
   ],
@@ -274,4 +286,4 @@
       "comment": "default value"
     }
   ]
-}
+}