brukerapi 0.1.9__py3-none-any.whl → 0.1.10__py3-none-any.whl

brukerapi/cli.py

@@ -62,7 +62,7 @@ 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",
@@ -81,7 +81,7 @@ 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",

brukerapi/dataset.py

@@ -461,7 +461,7 @@ class Dataset:
 
     def _sub_parameters(self, recipe):
         # entries with property e.g. VisuFGOrderDesc.nested to self._dataset['VisuFGOrderDesc'].nested
-        for match in re.finditer('#[a-zA-Z0-9_]+\.[a-zA-Z]+', recipe):
+        for match in re.finditer(r'#[a-zA-Z0-9_]+\.[a-zA-Z]+', recipe):
             m = re.match('#[a-zA-Z0-9_]+', match.group())
             recipe = recipe.replace(m.group(),"self['{}']".format(m.group()[1:]))
         # entries without property e.g. VisuFGOrderDesc to self._dataset['VisuFGOrderDesc'].value

brukerapi/jcampdx.py

@@ -8,18 +8,18 @@ import json
 
 SUPPORTED_VERSIONS = ['4.24', '5.0', '5.00 Bruker JCAMP library', '5.00 BRUKER JCAMP library', '5.01']
 GRAMMAR = {
-        'COMMENT_LINE' : '\$\$[^\n]*\n',
+        'COMMENT_LINE' : r'\$\$[^\n]*\n',
         'PARAMETER': '##',
-        'USER_DEFINED' : '\$',
-        'TRAILING_EOL' : '\n$',
-        'DATA_LABEL' : '\(XY..XY\)',
-        'DATA_DELIMETERS':', |\n',
-        'SIZE_BRACKET': '^\([^\(\)<>]*\)(?!$)',
+        'USER_DEFINED' : r'\$',
+        'TRAILING_EOL' : r'\n$',
+        'DATA_LABEL' : r'\(XY..XY\)',
+        'DATA_DELIMETERS': r', |\n',
+        'SIZE_BRACKET': r'^\([^\(\)<>]*\)(?!$)',
         'LIST_DELIMETER': ', ',
         'EQUAL_SIGN': '=',
-        'SINGLE_NUMBER':'-?[\d.]+(?:e[+-]?\d+)?',
-        'PARALLEL_BRACKET': '\) ',
-        'GEO_OBJ': '\(\(\([\s\S]*\)[\s\S]*\)[\s\S]*\)',
+        'SINGLE_NUMBER': r'-?[\d.]+(?:e[+-]?\d+)?',
+        'PARALLEL_BRACKET': r'\) ',
+        'GEO_OBJ': r'\(\(\([\s\S]*\)[\s\S]*\)[\s\S]*\)',
         'HEADER':'TITLE|JCAMPDX|JCAMP-DX|DATA TYPE|DATATYPE|ORIGIN|OWNER',
         'VERSION_TITLE':'JCAMPDX|JCAMP-DX'
     }
@@ -107,7 +107,7 @@ class Parameter(object):
 
     @property
     def key(self):
-        return re.sub('##', '', re.sub('\$', '', self.key_str)).rstrip()
+        return re.sub('##', '', re.sub(r'\$', '', self.key_str)).rstrip()
 
     @key.setter
     def key(self, key):
@@ -203,10 +203,10 @@ class GenericParameter(Parameter):
     @property
     def value(self, **kwargs):
 
-        val_str = re.sub('\n', '', self.val_str)
+        val_str = re.sub(r'\n', '', self.val_str)
 
         # unwrap wrapped list
-        if re.match('@[0-9]*\*',val_str) is not None:
+        if re.match(r'@[0-9]*\*',val_str) is not None:
             val_str = self._unwrap_list(val_str)
 
         val_str_list = GenericParameter.split_parallel_lists(val_str)
@@ -318,7 +318,7 @@ class GenericParameter(Parameter):
     @classmethod
     def parse_value(cls, val_str, size_bracket=None):
         # remove \n
-        val_str = re.sub('\n','', val_str)
+        val_str = re.sub(r'\n','', val_str)
 
         # sharp string
         if val_str.startswith('<') and val_str.endswith('>'):
@@ -455,12 +455,12 @@ class GenericParameter(Parameter):
 
     def _unwrap_list(self, val_str):
 
-        while re.search('@[0-9]*\*\(\d*\.?\d*\)', val_str):
-            match = re.search('@[0-9]*\*\(\d*\.?\d*\)', val_str)
+        while re.search(r'@[0-9]*\*\(-?\d*\.?\d*\)', val_str):
+            match = re.search(r'@[0-9]*\*\(-?\d*\.?\d*\)', val_str)
             left = val_str[0:match.start()]
             right = val_str[match.end():]
             sub = val_str[match.start():match.end()]
-            size, value = re.split('\*', sub)
+            size, value = re.split(r'\*', sub)
             size = int(size[1:])
             middle = ''
             for i in range(size):
@@ -506,7 +506,7 @@ class GeometryParameter(Parameter):
     #     :return: 4x4 3D Affine Transformation Matrix
     #     """
     #     # TODO support for multiple slice packages
-    #     match = re.match('\(\(\([^\)]*\)', self.val_str)
+    #     match = re.match(r'\(\(\([^\)]*\)', self.val_str)
     #     affine_str = self.val_str[match.start() + 3: match.end() - 1]
     #     orient, shift = affine_str.split(', ')
     #
@@ -799,7 +799,7 @@ class JCAMPDX(object):
             except:
                 raise InvalidJcampdxFile(path)
 
-        match = re.search('##{}[^\#\$]+|##\${}[^\#\$]+'.format(key,key), content)
+        match = re.search(r'##{}[^\#\$]+|##\${}[^\#\$]+'.format(key,key), content)
 
         if match == None:
             raise ParameterNotFound(key, path)
@@ -872,7 +872,7 @@ class JCAMPDX(object):
 
     @classmethod
     def split_key_value_pair(cls, line):
-        # ASSUMPTION the first occurence of = in jcampdx line divides key and value pair
+        # ASSUMPTION the first occurrence of = in jcampdx line divides key and value pair
         # example:
         match = re.search(GRAMMAR['EQUAL_SIGN'], line)
         key = line[0:match.start()]
@@ -903,10 +903,10 @@ class JCAMPDX(object):
 
     @classmethod
     def wrap_lines(cls, line):
-        line_wraps = re.split('\n', line)
+        line_wraps = re.split(r'\n', line)
         tail = line_wraps[-1]
 
-        tail_bits = re.split('\s', tail)
+        tail_bits = re.split(r'\s', tail)
 
         lines = 1
         tail = ''

brukerapi/schemas.py

@@ -491,12 +491,15 @@ class SchemaRawdata(Schema):
     def deserialize(self, data, layouts):
         return data[0::2,...] + 1j * data[1::2,...]
 
-    def seralize(self, data, layouts):
+    def serialize(self, data, layouts):
         data_ = np.zeros(layouts['shape_storage'], dtype=self.numpy_dtype, order='F')
         data_[0,...] = data.real
         data_[1, ...] = data.imag
         return data_
 
+# Compatibility alias for previous misspelling:
+SchemaRawdata.seralize = SchemaRawdata.serialize
+
 
 class SchemaSer(Schema):
 

brukerapi/splitters.py

@@ -136,7 +136,7 @@ class FrameGroupSplitter(Splitter):
         # number of samples in self.fg dimension
         fg_size = dataset.shape[fg_abs_index]
 
-        # If no index is specified, all elements of given dimension will be splited
+        # If no index is specified, all elements of given dimension will be split
         if select is None:
             select = list(range(0, fg_size))
 
@@ -266,9 +266,9 @@ class SlicePackageSplitter(Splitter):
         This functionality might be used for instance when converting data to a different data format.
 
         :param dataset: 2dseq dataset with multiple slice packages
-        :param write: if True, splitted data sets will we writen to drive
+        :param write: if True, split data sets will be written to drive
         :param path_out: a path to store data sets (optional)
-        :return: list of splitted data sets
+        :return: list of split data sets
         """
 
         try:
@@ -276,7 +276,7 @@ class SlicePackageSplitter(Splitter):
         except KeyError:
             print('Parameter VisuCoreSlicePacksSlices not found')
 
-        # list of splitted data sets
+        # list of split data sets
         datasets = []
 
         # range of frames of given slice package
@@ -303,7 +303,7 @@ class SlicePackageSplitter(Splitter):
             # construct a new Dataset, without loading data, the data will be supplied later
             dataset_ = Dataset(dataset.path.parents[1] / name, load=False)
 
-            # SPLIT parameteres
+            # SPLIT parameters
             dataset_.parameters = self._split_parameters(dataset, frame_range, fg_rel_index, fg_abs_index, sp_index, frame_count)
 
             # construct properties from the new set of parameters
@@ -391,4 +391,4 @@ class SlicePackageSplitter(Splitter):
         VisuCoreSlicePacksSliceDist = visu_pars_['VisuCoreSlicePacksSliceDist']
         value = int(VisuCoreSlicePacksSliceDist.value[sp_index])
         VisuCoreSlicePacksSliceDist.value = value
-        VisuCoreSlicePacksSliceDist.size = 1
+        VisuCoreSlicePacksSliceDist.size = 1

brukerapi-0.1.10.dist-info/METADATA

@@ -0,0 +1,227 @@
+Metadata-Version: 2.4
+Name: brukerapi
+Version: 0.1.10
+Summary: Bruker API
+Author-email: Tomas Psorn <tomaspsorn@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"
+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
+
+
+
+
+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
+"""""""""""""""""
+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 v360
+"""""""""""""""
+Compatible data set types:
+
+* **2dseq**
+* **rawdata.job0**
+* **rawdata.Navigator**
+

{brukerapi-0.1.9.dist-info → brukerapi-0.1.10.dist-info}/RECORD

@@ -1,13 +1,13 @@
 brukerapi/__init__.py,sha256=lT95qTFTZoyKk5vKYR3lPIdoLY6y4r8eOJcbk_wTy0g,83
-brukerapi/cli.py,sha256=2ABei7RcKh1yjXwjt1mjohhf_bs42KpcJ9VDgrs8xW0,4171
+brukerapi/cli.py,sha256=eHvbg7JHCRgS9LO8nkKplMu9q3ZDj03uvSGsqLZ4H0g,4167
 brukerapi/data.py,sha256=qdG404FHfWqk2g59E1qmtGpEghTKWcavt_kzvbo2WN8,203
-brukerapi/dataset.py,sha256=azPsK0Z_BzCPre4Wc3d_QQK50JiihLD_koY3T419U_w,25048
+brukerapi/dataset.py,sha256=otp-8N3n4HZc6IHp86PQ_2qXlPt3vzCdLiDYo3BviNk,25049
 brukerapi/exceptions.py,sha256=XHX6vtjPCqNMConAbT0IDjdiTIhHZe8kqjL12eBJ0Fg,9234
 brukerapi/folders.py,sha256=4JvAXbekqI0BTU3EBlSuObGio9wnKiuIm8Ggiprdjuw,17605
-brukerapi/jcampdx.py,sha256=WVTXJU4STAMz5aQXkmVp9ToU9PRLo2J9i9IDVpBKxYQ,25191
+brukerapi/jcampdx.py,sha256=he6Y0cdeMzbsg7Ls0UX3iQ37677YikNkEjGAr27aPws,25218
 brukerapi/mergers.py,sha256=IyNMesrhkdmexQgpO7vetaCJ-TSgN6zIatkLOv3mRMo,4067
-brukerapi/schemas.py,sha256=5-D67KjSchtWy65CJlfcXb4NdJB02UoVIYrEfulCyVc,24962
-brukerapi/splitters.py,sha256=idDwerSDs9MKrXpuTDEOsAiMxrBKL8_pd1rPX5b-g-E,15412
+brukerapi/schemas.py,sha256=o9c9PsxfZt0bYoeN4JXycSpAyRYOXocZXDTcnR9G-IY,25061
+brukerapi/splitters.py,sha256=GZFvuDryBiWL7u2QrldWyd3-5btmATaYpMynWJOPIwM,15402
 brukerapi/utils.py,sha256=kDKq1FV_E4mnROHALPEfv9aTfNy_QfIeZE6wB6IAn_E,1604
 brukerapi/config/properties_2dseq_core.json,sha256=3JlQyDWhRiczFhLTXR0NS1OIxWwRljDBRvwlBtUnsfg,3919
 brukerapi/config/properties_2dseq_custom.json,sha256=Kxic-Asg2am-vFtFHaHN_lxZdA8VEBUXlVeSPLbWLBw,9282
@@ -17,9 +17,9 @@ brukerapi/config/properties_rawdata_core.json,sha256=yksvjh5o4-t1e2VVzDSy_WuF5Qz
 brukerapi/config/properties_rawdata_custom.json,sha256=RBNvo1WzZ4oRRq0W9-hknpT7T8If536DEMBg9hyq_4o,2
 brukerapi/config/properties_traj_core.json,sha256=zx2gnPkVj9fUAL1iwixrtoRV7BlJpVTSYA4I-7s9Mzc,1956
 brukerapi/config/properties_traj_custom.json,sha256=-KWibjBW62-wbe6z28z9iK50kAIAyYxwtZZru37J1N4,4
-brukerapi-0.1.9.dist-info/LICENSE,sha256=qrKdH1kPjQsHQZxAS6dOSoPKyhrI0nKtNFVhG-fjDJw,1064
-brukerapi-0.1.9.dist-info/METADATA,sha256=yszIVM8jtQF-dUwXGXPkTHhJJzuut_OAM1k3PypSG1k,337
-brukerapi-0.1.9.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-brukerapi-0.1.9.dist-info/entry_points.txt,sha256=GkMTo84oMksVEhkrItYbnegKXFu0jyQHfOAvAn8z-Wo,46
-brukerapi-0.1.9.dist-info/top_level.txt,sha256=32V6nLorM2P3LQY_gPPKEgDbeTF0N-HCAyUeEUsf2GU,10
-brukerapi-0.1.9.dist-info/RECORD,,
+brukerapi-0.1.10.dist-info/licenses/LICENSE,sha256=qrKdH1kPjQsHQZxAS6dOSoPKyhrI0nKtNFVhG-fjDJw,1064
+brukerapi-0.1.10.dist-info/METADATA,sha256=sIQDg55peXquqazXBn75rj2QXVJcanAZEX3jpFfMH0U,5317
+brukerapi-0.1.10.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+brukerapi-0.1.10.dist-info/entry_points.txt,sha256=GkMTo84oMksVEhkrItYbnegKXFu0jyQHfOAvAn8z-Wo,46
+brukerapi-0.1.10.dist-info/top_level.txt,sha256=32V6nLorM2P3LQY_gPPKEgDbeTF0N-HCAyUeEUsf2GU,10
+brukerapi-0.1.10.dist-info/RECORD,,

{brukerapi-0.1.9.dist-info → brukerapi-0.1.10.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

brukerapi-0.1.9.dist-info/METADATA

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: brukerapi
-Version: 0.1.9
-Summary: Bruker API
-Home-page: https://github.com/isi-nmr/brukerapi-python
-Download-URL: https://github.com/isi-nmr/brukerapi-python/releases/latest
-Author: Tomas Psorn
-Author-email: tomaspsorn@isibrno.cz
-License: MIT
-License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: pyyaml
-