mdsh5


Namemdsh5 JSON
Version 0.0.3 PyPI version JSON
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SummaryA higher level python package that uses mdsthin to read MDSPlus data and store it in hdf5 formate for easy caching, viewing, distribution, and analysis.
upload_time2025-01-08 21:38:42
maintainerNone
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requires_python>=3.7
licenseApache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. 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keywords hdf5 mdsplus
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            # mdsh5
A higher level python package that uses [`mdsthin`](https://github.com/MDSplus/mdsthin) to read MDSPlus data and store it in hdf5 formate for easy caching, viewing, distribution, and analysis.

## Usage:


### No installation required
You can download the read_mds.py file from mdsh5 directory and use it directly or import it in your python code as per your need. You'll need to install `h5py`, `PyYaml`, and [`mdsthin`](https://github.com/MDSplus/mdsthin). For your convinience, a conda environment is provided in this repository to install the required packages in a separate environment. To use:

```
conda env create -f conda_env.yml
conda activate mdsh5
```

### Installation
If you plan to use this package often, you can install it locally using PyPi.
```
pip install mdsh5
```
This will also install a script `read_mds` in your `bin` that you can call as:
```
read_mds
```
No need to even write python and you can call this script from anywhere in your computer. Note that if you installed this package in a conda environment, the script would go to conda environment's bin directory which is typically present in `$HOME/anaconda3/envs/<env_name>/bin` and this might not be in your path by default.

## Purpose

If you want to run custom analysis on your shot data from the device, it can become tedious to download data using existing tools. To this end, [`mdsthin`](https://github.com/MDSplus/mdsthin) now provides an excellent pythonic solution to download MDSPlus data
from remote servers.

This package is one level higher data management tool. It uses [`mdsthin`](https://github.com/MDSplus/mdsthin) to download data but provides a functionality to provide required shot numbers, tree names, and point names in an organized yaml format and creates a fast transversible data dictionary in HDF5 format. HDF5 is simple self-describing fiole format which is supported on multiple platforms and has well developed libraries for reading and writing in almost all programming languages. The msot important aspect is that when python opens an HDF5 file, it can navigate through the data dictionary and read only the required portion of the data file. Thus it requires much less RAM and even if the accumulated data is in GigaBytes, you can read small particular portions of it very fast.

Additionally, if you use VSCode, I highly recomment installing the [H5Web extension](https://marketplace.visualstudio.com/items?itemName=h5web.vscode-h5web) which let's you quickly visualize the data stored in the HDF5 files created by this package.

![KSTAR_data](H5WebExample.png)

## Documentation

**NOTE:** All tree and pointnames will be converted to upper case regardless of how you enter them. This is a chosen convention to keep the cache consistent even if you change the case of a pointname.

Additional documentation would come soon. For now, please refer to the [config_examples](https://github.com/anchal-physics/mdsh5/tree/main/mdsh5/config_examples) to get started on how to provide the input configuration.

Additionally, use the help flag to print out the help message from `read_mds.py`:
```
(mdsh5)% python mdsh5/read_mds.py -h                          
usage: read_mds.py [-h] [-n SHOT_NUMBERS [SHOT_NUMBERS ...]] [-t TREES [TREES ...]] [-p POINT_NAMES [POINT_NAMES ...]] [-s SERVER] [-r RESAMPLE [RESAMPLE ...]] [--rescale RESCALE [RESCALE ...]] [-o OUT_FILENAME]
                   [--reread_data] [-v] [-c CONFIG] [--configTemplate]

Read data from MDSPlus server for porivded shot numbers, trees, and pointnames.

options:
  -h, --help            show this help message and exit
  -n SHOT_NUMBERS [SHOT_NUMBERS ...], --shot_numbers SHOT_NUMBERS [SHOT_NUMBERS ...]
                        Shot number(s)
  -t TREES [TREES ...], --trees TREES [TREES ...]
                        Tree name(s)
  -p POINT_NAMES [POINT_NAMES ...], --point_names POINT_NAMES [POINT_NAMES ...]
                        Point name(s). Must match number of trees provided unless a single tree is given.
  -s SERVER, --server SERVER
                        Server address. Default is None
  -r RESAMPLE [RESAMPLE ...], --resample RESAMPLE [RESAMPLE ...]
                        Resample signal(s) by providing a list of start, stop, and increment values. For negative value, enclose them withing double quotes and add a space at the beginning.Example: --resample " -0.1"
                        10.0 0.1
  --rescale RESCALE [RESCALE ...]
                        Rescale time dimension of trees to ensure that all of are in same units. Especially important if resample is used. Provide a rescaling factor to be multiplied by time axis for each tree provides
                        in trees option.Example: --resample " -0.1" 10.0 0.1
  -o OUT_FILENAME, --out_filename OUT_FILENAME
                        Output filename for saving data in file. Default is None. in which case it does not save files.
  --reread_data         Will overwrite on existing data for corresponding data entries in out_file. Default behavior is to skip readingpointnames whose data is present.
  -v, --verbose         Print verbose messages
  -c CONFIG, --config CONFIG
                        Configuration file containing shot_numbers, trees, point_names, server, and other settings. If provided, corresponding command line arguments are ignored.
  --configTemplate      If provided, configuration templates will be copied to current directory. All other arguments will be ignored.
```
Note that you can get configuration templates by using --configTemplate option and learn more by reading those files.

For queries, contanct Anchal Gupta (guptaa@fusion.gat.com).

## Required ssh configurations

This software does not take care of ssh tunneling often required to reach the "super secure" MDSPlus servers of various tokamaks in the world. Here I provide a simple language solution of what you would need to do:

If the MDSPlus server is only available in a closed of network whose gateway node is `gate.xyz.com`, add following to your `~/.ssh/config`:

```
Host <MDSPlusServerShortName> <MDSPlusServerFullAddress>
	Hostname <MDSPlusServerFullAddress>
	User <your_username>
	ProxyCommand ssh -q <GatewayNodeAddress> nc %h %p
```

It would be very useful if you can access the Gateway node without password. For setting that up, do:

### Create ssh key pair if you donot have it already
```
ssh-keygen -t rsa -b 4096 -C "your_email@domain.com"
```

### Copy the public key to Gateway node
```
ssh-copy-id remote_username@GatewayNodeAddress -i path_to_creates_ssh_id_file
```
This step will prompt you for password of the Gateway node. Once this step is completed,
you should be able to ssh into the gateway node without need of password using:
```
ssh remote_username@GatewayNodeAddress
```

### Add gateway to ssh config for ease (Optional)
```
Host <GatewayShortName> <GatewayNodeAddress>
  Hostname <GatewayNodeAddress>
  IdentityFile <path_to_creates_ssh_id_file>
  User <your_username>
  Port <required_port_if_different_from_22>
```

            

Raw data

            {
    "_id": null,
    "home_page": null,
    "name": "mdsh5",
    "maintainer": null,
    "docs_url": null,
    "requires_python": ">=3.7",
    "maintainer_email": null,
    "keywords": "HDF5, MDSPLus",
    "author": null,
    "author_email": "Anchal Gupta <anchal.physics@gmail.com>",
    "download_url": "https://files.pythonhosted.org/packages/ad/32/7ca2d18d7b26a4f1e8bfd44e17c433cc4ac978a38d696ead1cb70cfa0914/mdsh5-0.0.3.tar.gz",
    "platform": null,
    "description": "# mdsh5\nA higher level python package that uses [`mdsthin`](https://github.com/MDSplus/mdsthin) to read MDSPlus data and store it in hdf5 formate for easy caching, viewing, distribution, and analysis.\n\n## Usage:\n\n\n### No installation required\nYou can download the read_mds.py file from mdsh5 directory and use it directly or import it in your python code as per your need. You'll need to install `h5py`, `PyYaml`, and [`mdsthin`](https://github.com/MDSplus/mdsthin). For your convinience, a conda environment is provided in this repository to install the required packages in a separate environment. To use:\n\n```\nconda env create -f conda_env.yml\nconda activate mdsh5\n```\n\n### Installation\nIf you plan to use this package often, you can install it locally using PyPi.\n```\npip install mdsh5\n```\nThis will also install a script `read_mds` in your `bin` that you can call as:\n```\nread_mds\n```\nNo need to even write python and you can call this script from anywhere in your computer. Note that if you installed this package in a conda environment, the script would go to conda environment's bin directory which is typically present in `$HOME/anaconda3/envs/<env_name>/bin` and this might not be in your path by default.\n\n## Purpose\n\nIf you want to run custom analysis on your shot data from the device, it can become tedious to download data using existing tools. To this end, [`mdsthin`](https://github.com/MDSplus/mdsthin) now provides an excellent pythonic solution to download MDSPlus data\nfrom remote servers.\n\nThis package is one level higher data management tool. It uses [`mdsthin`](https://github.com/MDSplus/mdsthin) to download data but provides a functionality to provide required shot numbers, tree names, and point names in an organized yaml format and creates a fast transversible data dictionary in HDF5 format. HDF5 is simple self-describing fiole format which is supported on multiple platforms and has well developed libraries for reading and writing in almost all programming languages. The msot important aspect is that when python opens an HDF5 file, it can navigate through the data dictionary and read only the required portion of the data file. Thus it requires much less RAM and even if the accumulated data is in GigaBytes, you can read small particular portions of it very fast.\n\nAdditionally, if you use VSCode, I highly recomment installing the [H5Web extension](https://marketplace.visualstudio.com/items?itemName=h5web.vscode-h5web) which let's you quickly visualize the data stored in the HDF5 files created by this package.\n\n![KSTAR_data](H5WebExample.png)\n\n## Documentation\n\n**NOTE:** All tree and pointnames will be converted to upper case regardless of how you enter them. This is a chosen convention to keep the cache consistent even if you change the case of a pointname.\n\nAdditional documentation would come soon. For now, please refer to the [config_examples](https://github.com/anchal-physics/mdsh5/tree/main/mdsh5/config_examples) to get started on how to provide the input configuration.\n\nAdditionally, use the help flag to print out the help message from `read_mds.py`:\n```\n(mdsh5)% python mdsh5/read_mds.py -h                          \nusage: read_mds.py [-h] [-n SHOT_NUMBERS [SHOT_NUMBERS ...]] [-t TREES [TREES ...]] [-p POINT_NAMES [POINT_NAMES ...]] [-s SERVER] [-r RESAMPLE [RESAMPLE ...]] [--rescale RESCALE [RESCALE ...]] [-o OUT_FILENAME]\n                   [--reread_data] [-v] [-c CONFIG] [--configTemplate]\n\nRead data from MDSPlus server for porivded shot numbers, trees, and pointnames.\n\noptions:\n  -h, --help            show this help message and exit\n  -n SHOT_NUMBERS [SHOT_NUMBERS ...], --shot_numbers SHOT_NUMBERS [SHOT_NUMBERS ...]\n                        Shot number(s)\n  -t TREES [TREES ...], --trees TREES [TREES ...]\n                        Tree name(s)\n  -p POINT_NAMES [POINT_NAMES ...], --point_names POINT_NAMES [POINT_NAMES ...]\n                        Point name(s). Must match number of trees provided unless a single tree is given.\n  -s SERVER, --server SERVER\n                        Server address. Default is None\n  -r RESAMPLE [RESAMPLE ...], --resample RESAMPLE [RESAMPLE ...]\n                        Resample signal(s) by providing a list of start, stop, and increment values. For negative value, enclose them withing double quotes and add a space at the beginning.Example: --resample \" -0.1\"\n                        10.0 0.1\n  --rescale RESCALE [RESCALE ...]\n                        Rescale time dimension of trees to ensure that all of are in same units. Especially important if resample is used. Provide a rescaling factor to be multiplied by time axis for each tree provides\n                        in trees option.Example: --resample \" -0.1\" 10.0 0.1\n  -o OUT_FILENAME, --out_filename OUT_FILENAME\n                        Output filename for saving data in file. Default is None. in which case it does not save files.\n  --reread_data         Will overwrite on existing data for corresponding data entries in out_file. Default behavior is to skip readingpointnames whose data is present.\n  -v, --verbose         Print verbose messages\n  -c CONFIG, --config CONFIG\n                        Configuration file containing shot_numbers, trees, point_names, server, and other settings. If provided, corresponding command line arguments are ignored.\n  --configTemplate      If provided, configuration templates will be copied to current directory. All other arguments will be ignored.\n```\nNote that you can get configuration templates by using --configTemplate option and learn more by reading those files.\n\nFor queries, contanct Anchal Gupta (guptaa@fusion.gat.com).\n\n## Required ssh configurations\n\nThis software does not take care of ssh tunneling often required to reach the \"super secure\" MDSPlus servers of various tokamaks in the world. Here I provide a simple language solution of what you would need to do:\n\nIf the MDSPlus server is only available in a closed of network whose gateway node is `gate.xyz.com`, add following to your `~/.ssh/config`:\n\n```\nHost <MDSPlusServerShortName> <MDSPlusServerFullAddress>\n\tHostname <MDSPlusServerFullAddress>\n\tUser <your_username>\n\tProxyCommand ssh -q <GatewayNodeAddress> nc %h %p\n```\n\nIt would be very useful if you can access the Gateway node without password. For setting that up, do:\n\n### Create ssh key pair if you donot have it already\n```\nssh-keygen -t rsa -b 4096 -C \"your_email@domain.com\"\n```\n\n### Copy the public key to Gateway node\n```\nssh-copy-id remote_username@GatewayNodeAddress -i path_to_creates_ssh_id_file\n```\nThis step will prompt you for password of the Gateway node. Once this step is completed,\nyou should be able to ssh into the gateway node without need of password using:\n```\nssh remote_username@GatewayNodeAddress\n```\n\n### Add gateway to ssh config for ease (Optional)\n```\nHost <GatewayShortName> <GatewayNodeAddress>\n  Hostname <GatewayNodeAddress>\n  IdentityFile <path_to_creates_ssh_id_file>\n  User <your_username>\n  Port <required_port_if_different_from_22>\n```\n",
    "bugtrack_url": null,
    "license": "Apache License Version 2.0, January 2004 http://www.apache.org/licenses/  TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION  1. Definitions.  \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.  \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.  \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.  \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License.  \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files.  \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types.  \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below).  \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.  \"Contribution\" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, \"submitted\" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as \"Not a Contribution.\"  \"Contributor\" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work.  2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form.  3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed.  4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions:  (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and  (b) You must cause any modified files to carry prominent notices stating that You changed the files; and  (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and  (d) If the Work includes a \"NOTICE\" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.  You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.  5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. 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