nmrPype


NamenmrPype JSON
Version 1.0.8 PyPI version JSON
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home_pageNone
SummaryPython implementation of Nuclear Magnetic Resonance (NMR) signal analysis program "nmrPipe"
upload_time2025-02-04 16:01:02
maintainerNone
docs_urlNone
authorMicah Smith
requires_python>=3.10
licenseCopyright Notice and Statement for the nmrPype project Copyright (c) 2023-2024 Micah J. Smith All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: a. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. b. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. c. Neither the name of the author nor the names of contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Copyright Notice and Statement for the nmrglue Project Copyright (c) 2010-2015 Jonathan J. Helmus All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: a. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. b. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. c. Neither the name of the author nor the names of contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
keywords nmr decomposition
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            # nmrPype
Python implementation of command-line program nmrpipe, using linux pipelines to process NMR data.

- **Documentation:** https://phimykah.github.io/nmrpype
- **NMRPipe Website:** https://www.ibbr.umd.edu/nmrpipe
- **Source Code:** https://github.com/PhiMykah/nmrPype
- **Bug Reports:** https://github.com/PhiMykah/nmrPype/issues

Installation
============
Installing nmrPype can be done by through pip:
```sh
# Install prerequisites
pip install numpy scipy
# Install program
pip install nmrPype
``` 
A virtual environment or conda environment is recommended for using nmrPype.
If using conda, `numpy` and `scipy` can be installed using `conda install`.

### Note

This is made for Python 3.10 or above. Some of the code requires Python 3.10's features such as `match-case` statements. 

Python 3.12 is recommended as development is done with 3.12, but testing is done to assure that 3.10 is supported.

Usage
==========
nmrPype can be used in through two methods: Command-line and Script

Command-line
--------------
```
nmrPype -in [inFile] -fn fnName -out [outFile] [-ov]
```
Functions:
```
FT                  Perform a Fourier transform (FT) on the data
ZF                  Perform a Zero Fill (ZF) Operation on the data
SP (SINE)           Adjustable Sine Bell
PS                  Perform a Phase Correction (PS) on the data
YTP (TP, XY2YX)     2D Plane Transpose
ZTP (XYZ2ZYX)       3D Matrix Transpose
ATP (XYZA2AYZX)     4D Matrix Transpose (unimplemented)
NULL                Null Function, does not apply any function
```
Run the `nmrPype --help` command to see a list of more options.

Script
------
In a Python script or jupyter notebook use the following line:
```py
import nmrPype
```
I recommend setting the import as `pype` for simplification.
### Example
```py
import nmrPype as pype

df = pype.DataFrame("h.fid") # Load NMR data file into script
df.array() # Display spectral data array
```

Building From Source
====================

### Building using Pip

1. Install prerequisites
```sh
pip install numpy scipy
```
2. Clone the repository
```sh
git clone https://github.com/PhiMykah/nmrPype
```
3. Install in development mode with pip:

```sh
cd nmrPype
pip install -e .
```

### Building using Conda

With conda, the environment.yml file can be used to obtain
the development environment.

1. Clone the repository
```sh
git clone https://github.com/PhiMykah/nmrPype
```
2. Copy the source conda environment
```sh
cd nmrPype
conda env create -f environment.yml --name nmrpype
```
- You can set the name to anything you wish, but typically
my convention is to have the environments lowercase

3. Install in development mode with pip:
```
pip install -e .
```


            

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    "description": "# nmrPype\r\nPython implementation of command-line program nmrpipe, using linux pipelines to process NMR data.\r\n\r\n- **Documentation:** https://phimykah.github.io/nmrpype\r\n- **NMRPipe Website:** https://www.ibbr.umd.edu/nmrpipe\r\n- **Source Code:** https://github.com/PhiMykah/nmrPype\r\n- **Bug Reports:** https://github.com/PhiMykah/nmrPype/issues\r\n\r\nInstallation\r\n============\r\nInstalling nmrPype can be done by through pip:\r\n```sh\r\n# Install prerequisites\r\npip install numpy scipy\r\n# Install program\r\npip install nmrPype\r\n``` \r\nA virtual environment or conda environment is recommended for using nmrPype.\r\nIf using conda, `numpy` and `scipy` can be installed using `conda install`.\r\n\r\n### Note\r\n\r\nThis is made for Python 3.10 or above. Some of the code requires Python 3.10's features such as `match-case` statements. \r\n\r\nPython 3.12 is recommended as development is done with 3.12, but testing is done to assure that 3.10 is supported.\r\n\r\nUsage\r\n==========\r\nnmrPype can be used in through two methods: Command-line and Script\r\n\r\nCommand-line\r\n--------------\r\n```\r\nnmrPype -in [inFile] -fn fnName -out [outFile] [-ov]\r\n```\r\nFunctions:\r\n```\r\nFT                  Perform a Fourier transform (FT) on the data\r\nZF                  Perform a Zero Fill (ZF) Operation on the data\r\nSP (SINE)           Adjustable Sine Bell\r\nPS                  Perform a Phase Correction (PS) on the data\r\nYTP (TP, XY2YX)     2D Plane Transpose\r\nZTP (XYZ2ZYX)       3D Matrix Transpose\r\nATP (XYZA2AYZX)     4D Matrix Transpose (unimplemented)\r\nNULL                Null Function, does not apply any function\r\n```\r\nRun the `nmrPype --help` command to see a list of more options.\r\n\r\nScript\r\n------\r\nIn a Python script or jupyter notebook use the following line:\r\n```py\r\nimport nmrPype\r\n```\r\nI recommend setting the import as `pype` for simplification.\r\n### Example\r\n```py\r\nimport nmrPype as pype\r\n\r\ndf = pype.DataFrame(\"h.fid\") # Load NMR data file into script\r\ndf.array() # Display spectral data array\r\n```\r\n\r\nBuilding From Source\r\n====================\r\n\r\n### Building using Pip\r\n\r\n1. Install prerequisites\r\n```sh\r\npip install numpy scipy\r\n```\r\n2. Clone the repository\r\n```sh\r\ngit clone https://github.com/PhiMykah/nmrPype\r\n```\r\n3. Install in development mode with pip:\r\n\r\n```sh\r\ncd nmrPype\r\npip install -e .\r\n```\r\n\r\n### Building using Conda\r\n\r\nWith conda, the environment.yml file can be used to obtain\r\nthe development environment.\r\n\r\n1. Clone the repository\r\n```sh\r\ngit clone https://github.com/PhiMykah/nmrPype\r\n```\r\n2. Copy the source conda environment\r\n```sh\r\ncd nmrPype\r\nconda env create -f environment.yml --name nmrpype\r\n```\r\n- You can set the name to anything you wish, but typically\r\nmy convention is to have the environments lowercase\r\n\r\n3. Install in development mode with pip:\r\n```\r\npip install -e .\r\n```\r\n\r\n",
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