brukerapi 0.1.9__tar.gz → 0.2.0__tar.gz

brukerapi-0.2.0/PKG-INFO

@@ -0,0 +1,244 @@
+Metadata-Version: 2.4
+Name: brukerapi
+Version: 0.2.0
+Summary: Bruker API
+Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, 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
+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: pyyaml
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: zenodo_get; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Dynamic: license-file
+
+brukerapi-python
+======================
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3831320.svg
+   :target: https://doi.org/10.5281/zenodo.3831320
+
+.. image:: https://github.com/isi-nmr/brukerapi-python/workflows/CI/badge.svg
+   :target: https://doi.org/10.5281/zenodo.3831320
+
+.. image:: https://readthedocs.org/projects/bruker-api/badge/?version=latest
+    :target: https://bruker-api.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+
+A Python package providing I/O interface for Bruker data sets.
+
+tl;dr
+========
+
+Install using pip:
+
+.. code-block:: shell
+
+    pip install brukerapi
+
+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.data                         # access data array
+    dataset.VisuCoreSize                 # get a value of a single parameter
+
+Load an entire **study**:
+
+.. code-block:: python
+
+    from brukerapi.folders import 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
+
+Load a parametric file:
+
+.. code-block:: python
+
+   from brukerapi.jcampdx import JCAMPDX
+
+   parameters = JCAMPDX('path_to_scan/method')
+   
+   TR = data.params["PVM_RepetitionTime"].value # This way
+   TR = data.get_value("PVM_RepetitionTime") # Or this way
+
+
+
+
+
+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)
+
+Examples
+========
+
+* How to `read <examples/read_fid.ipynb>`_ a Bruker fid, 2dseq, rawdata, or ser 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
+
+Documentation
+==============
+
+Online `documentation <https://bruker-api.readthedocs.io/en/latest/>`_ of the API is available at Read The Docs.
+
+
+Install
+=======
+Using pip:
+
+.. code-block:: shell
+
+    pip install brukerapi
+
+From source:
+
+.. code-block:: shell
+
+    git clone https://github.com/isi-nmr/brukerapi-python.git
+    cd brukerapi-python
+    python setup.py build
+    python setup.py install
+
+Testing
+========
+To ensure reliability, every commit to this repository is tested against the following, publicly available
+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>`_
+
+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**
+

{brukerapi-0.1.9 → brukerapi-0.2.0}/README.rst

@@ -11,6 +11,7 @@ brukerapi-python
     :target: https://bruker-api.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
+
 A Python package providing I/O interface for Bruker data sets.
 
 tl;dr
@@ -51,6 +52,18 @@ Load an entire **study**:
     dataset.data                       # access data array
     dataset.VisuCoreSize               # get a value of a single parameter
 
+Load a parametric file:
+
+.. code-block:: python
+
+   from brukerapi.jcampdx import JCAMPDX
+
+   parameters = JCAMPDX('path_to_scan/method')
+   
+   TR = data.params["PVM_RepetitionTime"].value # This way
+   TR = data.get_value("PVM_RepetitionTime") # Or this way
+
+
 
 
 
@@ -151,8 +164,8 @@ Compatible pulse sequences for **fid** data sets:
 * STEAM.ppg
 * igFLASH.ppg
 
-ParaVision v6.0.1
-"""""""""""""""""
+ParaVision v6.0.1 and v7.0.0
+"""""""""""""""""""""""""""""""
 Compatible data set types:
 
 * **fid**
@@ -198,8 +211,10 @@ Compatible pulse sequences for **fid** data sets:
 * CPMG.ppg
 * RfProfile.ppg
 
-ParaVision v360
-"""""""""""""""
+
+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**

{brukerapi-0.1.9 → brukerapi-0.2.0}/brukerapi/cli.py

@@ -1,18 +1,17 @@
-from argparse import ArgumentParser
-from brukerapi.splitters import *
-from brukerapi.folders import *
 import sys
+from argparse import ArgumentParser
 
+from brukerapi.folders import Dataset, Filter, Folder, Path
+from brukerapi.splitters import FrameGroupSplitter, SlicePackageSplitter
 
-def main():
-    """
 
-    """
-    parser = ArgumentParser(prog='bruker')
+def main():
+    """ """
+    parser = ArgumentParser(prog="bruker")
     subparsers = parser.add_subparsers()
 
     # report sub-command
-    parser_report = subparsers.add_parser('report', help='export properties of data sets to json, or yaml file')
+    parser_report = subparsers.add_parser("report", help="export properties of data sets to json, or yaml file")
     parser_report.add_argument(
         "-i",
         "--input",
@@ -27,27 +26,22 @@ def main():
     parser_report.add_argument(
         "-f",
         "--format",
-        choices=['json', 'yml'],
-        default='json',
+        choices=["json", "yml"],
+        default="json",
         help="Format of report files",
     )
     parser_report.add_argument(
         "-p",
         "--props",
         type=str,
-        nargs='+',
+        nargs="+",
         help="List of properties to include",
     )
-    parser_report.add_argument(
-        "-v",
-        "--verbose",
-        help="make verbose",
-        action="store_true"
-    )
+    parser_report.add_argument("-v", "--verbose", help="make verbose", action="store_true")
     parser_report.set_defaults(func=report)
 
     # report sub-command
-    parser_split = subparsers.add_parser('split', help='split dataset into several sub-datasets')
+    parser_split = subparsers.add_parser("split", help="split dataset into several sub-datasets")
     parser_split.add_argument(
         "-i",
         "--input",
@@ -62,13 +56,13 @@ def main():
         dest="path_out",
         type=str,
         required=False,
-        help="Folder to save splitted data sets",
+        help="Folder to save split data sets",
     )
     parser_split.add_argument(
         "-s",
         "--slice_package",
         dest="slice_package",
-        action='store_true',
+        action="store_true",
         help="Split by slice package",
     )
     parser_split.add_argument(
@@ -81,7 +75,7 @@ def main():
     parser_split.set_defaults(func=split)
 
     # filter sub-command
-    parser_filter = subparsers.add_parser('filter', help='get files based on querry')
+    parser_filter = subparsers.add_parser("filter", help="get files based on query")
     parser_filter.add_argument(
         "-i",
         "--input",
@@ -108,8 +102,6 @@ def main():
     func(args)
 
 
-
-
 def split(args):
     """
     split sub-command
@@ -145,13 +137,12 @@ def report(args):
         elif output.is_dir():
             # folder to folder
             Folder(input).report(path_out=output, format_=args.format, props=args.props, verbose=args.verbose)
-    else:
-        # dataset in-place
-        if 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():
-            Dataset(input, add_parameters=['subject']).report(path=output, 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 to folder, or dataset to file
+    elif output.is_dir():
+        Dataset(input, add_parameters=["subject"]).report(path=output, props=args.props, verbose=args.verbose)
 
 
 def filter(args):

{brukerapi-0.1.9 → brukerapi-0.2.0}/brukerapi/config/properties_fid_core.json

@@ -223,9 +223,7 @@
         ["#PULPROG[1:-1]",
           [
             "EPI.ppg",
-            "DtiEpi.ppg",
             "navigatorEPI_OM.ppg",
-            "EPSI.ppg",
             "FAIR_EPI.ppg",
             "CASL_EPI.ppg",
             "T1_EPI.ppg",
@@ -236,6 +234,18 @@
         "#ACQ_sw_version in ['<PV 5.1>', '<PV 6.0>', '<PV 6.0.1>', '<PV-7.0.0>']"
       ]
     },
+    {
+      "cmd": "'dEPI'" ,
+      "conditions": [
+        ["#PULPROG[1:-1]",
+          [
+            "DtiEpi.ppg",
+            "EPSI.ppg"
+          ]
+        ],
+        "#ACQ_sw_version in ['<PV 5.1>', '<PV 6.0>', '<PV 6.0.1>', '<PV-7.0.0>']"
+      ]
+    },
     {
       "cmd": "'SPECTROSCOPY'" ,
       "conditions": [
@@ -322,7 +332,13 @@
       ]
     },
     {
-      "cmd": "#NR",
+      "cmd": "#NSegments*#NI*#NR*(#ACQ_size[2] if len(#ACQ_size)>2 else 1)",
+      "conditions": [
+        "@scheme_id=='dEPI'"
+      ]
+    },
+    {
+      "cmd": "#NR*#NI",
       "conditions": [
         "@scheme_id=='SPECTROSCOPY'"
       ]
@@ -430,9 +446,23 @@
         "@scheme_id=='EPI'"
       ]
     },
+    {
+      "cmd": [
+        "#PVM_EncMatrix[0] * #PVM_EncMatrix[1] // #NSegments",
+        "#PVM_EncNReceivers",
+        "#NSegments",
+        "#NI",
+        "#NR",
+        "#ACQ_size[2] if len(#ACQ_size)>2 else 1"
+      ],
+      "conditions": [
+        "@scheme_id=='dEPI'"
+      ]
+    },
     {
       "cmd": [
         "#ACQ_size.tuple[0] // 2",
+        "#NI",
         "#NR"
       ],
       "conditions": [
@@ -527,11 +557,24 @@
     {
       "cmd": [0,2,3,4,1],
       "conditions": [
-        "@scheme_id in ['EPI', 'SPIRAL']"
+        "@scheme_id in ['SPIRAL']"
+      ]
+    },
+    {
+      "cmd": [0,2,3,4,1],
+      "conditions": [
+        "@scheme_id in ['EPI']"
+      ]
+    },
+    {
+      "cmd": [0,2,3,4,1,5],
+      "conditions": [
+        "@scheme_id in ['dEPI']"
       ]
     },
+    
     {
-      "cmd": [0,1],
+      "cmd": [0,1,2],
       "conditions": [
         "@scheme_id=='SPECTROSCOPY'"
       ]
@@ -604,9 +647,23 @@
         "@scheme_id=='EPI'"
       ]
     },
+    {
+      "cmd": [
+        "#PVM_EncMatrix[0]",
+        "#PVM_EncMatrix[1]",
+        "#NI",
+        "#NR",
+        "#PVM_EncNReceivers",
+        "#ACQ_size[2] if len(#ACQ_size)>2 else 1"
+      ],
+      "conditions": [
+        "@scheme_id=='dEPI'"
+      ]
+    },
     {
       "cmd": [
         "#ACQ_size.tuple[0] // 2",
+        "#NI",
         "#NR"
       ],
       "conditions": [
@@ -701,7 +758,7 @@
         "'channel'"
       ],
       "conditions": [
-        ["@scheme_id",["CART_2D","RADIAL","EPI","SPIRAL","ZTE"]]
+        ["@scheme_id",["CART_2D","RADIAL","EPI","dEPI","SPIRAL","ZTE"]]
       ]
     },
     {

{brukerapi-0.1.9 → brukerapi-0.2.0}/brukerapi/config/properties_rawdata_core.json

@@ -5,7 +5,7 @@
         "conditions": [
           "#GO_raw_data_format=='GO_32BIT_SGN_INT'",
           "#BYTORDA=='little'",
-          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
+          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
         ]
     },
     {
@@ -13,7 +13,7 @@
         "conditions": [
           "#GO_raw_data_format=='GO_16BIT_SGN_INT'",
           "#BYTORDA=='little'",
-          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
+          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
         ]
     },
     {
@@ -21,7 +21,7 @@
         "conditions": [
           "#GO_raw_data_format=='GO_32BIT_FLOAT'",
           "#BYTORDA=='little'",
-          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
+          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
         ]
     },
     {
@@ -29,7 +29,7 @@
         "conditions": [
           "#GO_raw_data_format=='GO_32BIT_SGN_INT'",
           "#BYTORDA=='big'",
-          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
+          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
         ]
     },
     {
@@ -37,7 +37,7 @@
         "conditions": [
           "#GO_raw_data_format=='GO_16BIT_SGN_INT'",
           "#BYTORDA=='big'",
-          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
+          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
         ]
     },
     {
@@ -45,7 +45,7 @@
         "conditions": [
           "#GO_raw_data_format=='GO_32BIT_FLOAT'",
           "#BYTORDA=='big'",
-          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
+          ["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
         ]
     },
     {
@@ -53,7 +53,7 @@
         "conditions": [
           "#ACQ_word_size=='_32_BIT'",
           "#BYTORDA=='little'",
-          ["#ACQ_sw_version",["<PV-360.1.1>"]]
+          ["#ACQ_sw_version",["<PV-360.1.1>","<PV-360.3.0>","<PV-360.3.1>","<PV-360.3.2>","<PV-360.3.3>","<PV-360.3.4>","<PV-360.3.5>","<PV-360.3.6>","<PV-360.3.7>"]]
         ]
     }
   ],
@@ -61,9 +61,16 @@
     {
       "cmd": "#ACQ_jobs.primed_dict(7)['<{}>'.format(@subtype)]",
       "conditions": [
-        "#ACQ_sw_version in ['<PV-360.1.1>']"
+        ["#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",["<PV-360.3.0>","<PV-360.3.1>","<PV-360.3.2>","<PV-360.3.3>","<PV-360.3.4>","<PV-360.3.5>","<PV-360.3.6>","<PV-360.3.7>"]]
+      ]
+    },
+
     {
       "cmd": "#ACQ_jobs.nested[0]",
       "conditions": [
@@ -88,7 +95,7 @@
   ],
   "shape_storage": [
     {
-      "cmd": "(@job_desc[0],) + (@job_desc[3],)",
+      "cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[3],)",
       "conditions": []
     }
   ]

brukerapi-0.2.0/brukerapi/config/properties_rawdata_custom.json

@@ -0,0 +1,65 @@
+{
+  "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": "f'RawData_{@subtype}_{@exp_id}_{@subj_id}_{@study_id}'",
+      "conditions": [
+      ]
+    }
+  ],
+  "TR": [
+    {
+        "cmd": "#PVM_RepetitionTime",
+        "conditions": [],
+        "unit": "ms"
+    }
+  ],
+  "TE": [
+    {
+        "cmd": "#PVM_EchoTime",
+        "conditions": [],
+        "unit": "ms"
+    }
+  ]
+}

{brukerapi-0.1.9 → brukerapi-0.2.0}/brukerapi/data.py

@@ -1,8 +1,7 @@
-class DataRandomAccess():
-
+class DataRandomAccess:
     def __init__(self, dataset):
         self._dataset = dataset
         self._scheme = dataset._scheme
 
     def __getitem__(self, slice):
-        return self._scheme.ra(slice)
+        return self._scheme.ra(slice)