brukerapi 0.1.9__py3-none-any.whl → 0.2.0__py3-none-any.whl

brukerapi-0.2.0.dist-info/METADATA

@@ -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-0.2.0.dist-info/RECORD

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{brukerapi-0.1.9.dist-info → brukerapi-0.2.0.dist-info}/WHEEL

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 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
-

brukerapi-0.1.9.dist-info/RECORD

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