vaft 0.1__tar.gz

vaft-0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: vaft
+Version: 0.1
+Summary: Versatile Analytical Framework for Tokamak
+Home-page: https://github.com/VEST-Tokamak/vaft
+Author: satelite2517, Hikitonic
+Author-email: satelite2517@snu.ac.kr, peppertonic18@snu.ac.kr
+Requires-Dist: h5py
+Requires-Dist: numpy
+Requires-Dist: uncertainties
+Requires-Dist: omas
+Requires-Dist: matplotlib
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"

vaft-0.1/README.md

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+# VAFT(Versatile Analytical Framework for Tokamak) 
+
+All users are allowed to read these datasets, but if modification/deletion permissions are needed, please contact email. Databse system uses HSDS and if you want to get the h5 file format follow [h5pyd github](https://github.com/HDFGroup/h5pyd). This repository utilizes hdf5 and ODS data strucure ([omas github](https://github.com/gafusion/omas?tab=readme-ov-file)), if you need more information about this structure can be found on the following website: [omas](https://gafusion.github.io/omas/).
+
+## Usage
+
+follow the [Learn Usage](https://satelite2517.github.io/vaft/)
+
+
+## Reporting bugs
+
+Leave comment on [issue](https://github.com/satelite2517/vaft/issues) or mail us (satelite2517@snu.ac.kr, peppertonic18@snu.ac.kr)
+If you need more infomation about VEST find [Nuplex](http://nuplex.snu.ac.kr)

vaft-0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

vaft-0.1/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name="vaft",
+    version="0.1",
+    packages=find_packages(),
+    description="Versatile Analytical Framework for Tokamak",
+    author="satelite2517, Hikitonic",
+    author_email="satelite2517@snu.ac.kr, peppertonic18@snu.ac.kr",
+    url="https://github.com/VEST-Tokamak/vaft",
+    install_requires=[
+        "h5py",
+        "numpy",
+        "uncertainties",
+        "omas",
+        "matplotlib",
+    ],
+    extras_require={
+        "dev": [
+            "pytest",
+            "black",
+            "flake8",
+        ],
+    },
+)

vaft-0.1/test/test_change_time_convention.py

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+import vaft
+import pkg_resources
+from omas import *
+
+# load sample ods from file
+data_path = pkg_resources.resource_filename('vaft', 'data/41514.h5')
+ods = load_omas_h5(data_path, consistency_check=False)
+
+# change time convention
+

vaft-0.1/test/test_import.py

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+import vaft
+from vaft.process import *
+from vaft.plot import *
+from vaft.machine_mapping import *
+from vaft.formula import *
+from vaft.omas import *
+from vaft.code import *
+from vaft.database import *
+from vaft.database.file import *
+from vaft.database.raw import *
+# from vaft.database.ods import * 
+# Traceback (most recent call last):
+#   File "/Users/yun/Library/CloudStorage/OneDrive-Personal/Documents/Research/Code/vaft/test/test_import.py", line 11, in <module>
+#     from vaft.database.ods import *
+#   File "/Users/yun/Library/CloudStorage/OneDrive-Personal/Documents/Research/Code/vaft/vaft/database/ods/__init__.py", line 1, in <module>
+#     from .default import *
+#   File "/Users/yun/Library/CloudStorage/OneDrive-Personal/Documents/Research/Code/vaft/vaft/database/ods/default.py", line 23, in <module>
+#     def exist_file(username=h5pyd.getServerInfo()['username'], shot=None):
+#   File "/Users/yun/miniforge3/envs/fusion/lib/python3.8/site-packages/h5pyd/_hl/serverinfo.py", line 37, in getServerInfo
+#     http_conn = HttpConn(
+#   File "/Users/yun/miniforge3/envs/fusion/lib/python3.8/site-packages/h5pyd/_hl/httpconn.py", line 205, in __init__
+
+print(f"vaft version: {vaft.__version__}")

vaft-0.1/test/test_load_sample.py

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+import vest
+import pkg_resources
+from omas import *
+
+# load sample ods from file
+data_path = pkg_resources.resource_filename('vest', 'data/39915.json')
+
+# load the ods file
+ods = ODS()
+ods = ods.load(data_path, consistency_check=False)
+
+# print the ods keys
+print(ods.keys())
+
+# print the ods['equilibrium'] keys
+print(ods['equilibrium'].keys())
+

vaft-0.1/test/test_plot_submodule.py

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+# in this file, we test the all available plot submodule functions
+# we will use the sample ods file in the data folder
+from omas import *
+import vaft
+import pkg_resources
+
+data_path = pkg_resources.resource_filename('vest', 'data/39915.json')
+# load sample ods from file
+ods = ODS()
+ods = ods.load(data_path, consistency_check=False)
+
+# plot pf_active
+vaft.plot.time_pf_active_all_current(ods)
+

vaft-0.1/vaft/__init__.py

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+# Top-level package initialization
+from .version import __version__
+
+__all__ = ['process', 'formula', 'machine_mapping', 'plot', 'omas', 'code', 'database']
+
+from . import process
+from . import formula
+from . import machine_mapping
+from . import plot
+from . import omas
+from . import code
+from . import database

vaft-0.1/vaft/code/__init__.py

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+from . import *

vaft-0.1/vaft/database/__init__.py

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+from .ods import *
+from .raw import *

vaft-0.1/vaft/database/ods.py

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+import requests
+import urllib3
+import h5pyd, h5py
+import omas
+import subprocess
+import numpy
+from uncertainties import ufloat
+from uncertainties.unumpy import uarray
+
+
+def is_connect():
+    """
+    Check if the user is connected to the server.
+    
+    input: None
+    output: True if the user is connected to the server, False otherwise.
+
+    """
+    try:
+        if h5pyd.getServerInfo()['state']=='READY':
+            username = h5pyd.getServerInfo()['username']
+            return True 
+        else:
+            return False
+    except requests.exceptions.ConnectTimeout:
+        return False
+    
+
+def exist_file(username=h5pyd.getServerInfo()['username'], shot=None):
+    """
+    Check if the file exists.
+
+    If the 'username' or 'shot' parameter is provided, the function will check if a file with a matching prefix exists.
+    If 'username' or 'shot' is not provided, the function will list all files in the user's folder.
+    
+    Parameters:
+        username (str): The username to access the corresponding folder.
+        shot (int, optional): The shot number to search for (default is None).
+    
+    Returns:
+        bool: True if the file or folder exists, False if it does not or if a connection error occurs.
+    """
+    try:
+        Folder = list(h5pyd.Folder("/" + username + "/"))
+        if shot is not None:
+            file_list = list(Folder)
+            file_exist = False  
+
+            for file in file_list:
+                if file.split("_")[0] == str(shot):
+                    file_exist = True
+                    print(file)
+                    return True
+            
+            if not file_exist:
+                print("File does not exist")
+                return False
+        else:
+            print(list(Folder))
+    except urllib3.exceptions.MaxRetryError:
+        return False
+    return True
+
+def save(ods, shot, filename=None, env='server'):
+    """
+    Function to save an ODS (Open Data Structure) file either locally or to an HDF5 server.
+
+    This function handles saving the ODS data to an HDF5 file, either on the local file system or
+    remotely to an HDF5 server using the `hsload` command. If no filename is provided, the function 
+    defaults to using the shot number with an `.h5` extension.
+
+    Parameters:
+    ods (object): The Open Data Structure (ODS) object that needs to be saved.
+    shot (int): The shot number associated with the ODS data, used to generate the filename if not provided.
+    filename (str, optional): The name of the file to save the ODS data. Defaults to `None`, which generates a name based on the shot number.
+    env (str, optional): The environment where the file will be saved. It can be either 'server' for server upload or 'local' for local storage. Defaults to 'server'.
+
+    Returns:
+    None: The function doesn't return any specific value but prints information about the saving process.
+    """
+
+    # If no filename is provided, use the shot number to create a default file name
+    if filename is None:
+        filename = str(shot) + '.h5'
+
+    # If the environment is 'local', save the file locally using OMAS
+    if env == 'local':
+        omas.save_omas_h5(ods, filename)
+
+    # Test the connection to the server, and exit if the connection fails
+    if is_connect() != True:
+        print('Error: Connection to the server failed')
+        return
+    
+    # Get the current username from the HDF5 server and construct the file path
+    username = 'public' if h5pyd.getServerInfo()['username'] == 'admin' else h5pyd.getServerInfo()['username']
+    file_path = "hdf5://{}/{}".format(username, filename)
+    omas.save_omas_h5(ods, filename)
+
+    command = ['hsload', '--h5image', filename, file_path]
+    result = subprocess.run(command, capture_output=True, text=True)
+
+    subprocess.run(['rm', filename], capture_output=True, text=True)
+
+def convertDataset(ods, data):
+    """
+    Recursive utility function to map HDF5 structure to ODS
+
+    :param ods: input ODS to be populated
+
+    :param data: HDF5 dataset of group
+    """
+    import h5py
+
+    keys = data.keys()
+    try:
+        keys = sorted(list(map(int, keys)))
+    except ValueError:
+        pass
+    for oitem in keys:
+        item = str(oitem)
+        if item.endswith('_error_upper'):
+            continue
+        if isinstance(data[item], h5py.Dataset):
+            if item + '_error_upper' in data:
+                if isinstance(data[item][()], (float, numpy.floating)):
+                    ods.setraw(item, ufloat(data[item][()], data[item + '_error_upper'][()]))
+                else:
+                    ods.setraw(item, uarray(data[item][()], data[item + '_error_upper'][()]))
+            else:
+                ods.setraw(item, data[item][()])
+        elif isinstance(data[item], h5py.Group):
+            convertDataset(ods.setraw(oitem, ods.same_init_ods()), data[item])
+
+def load(shot, directory=None):
+
+    if isinstance(shot, list):
+        shot_list = shot
+        ods_list = []
+        for shot in shot_list:
+            ods = omas.ODS()
+            if directory is None:
+                filename = f'hdf5://public/{shot}.h5'
+            else:
+                filename = f'hdf5://{directory}/{shot}.h5'
+            with h5py.File(h5pyd.H5Image(filename)) as data:
+                convertDataset(ods, data)
+            ods_list.append(ods)
+        return ods_list
+
+    else:
+        ods = omas.ODS()
+        shot_list = [int(shot)]
+        if directory is None:
+            filename = f'hdf5://public/{shot}.h5'
+        else:
+            filename = f'hdf5://{directory}/{shot}.h5'
+        with h5py.File(h5pyd.H5Image(filename)) as data:
+            convertDataset(ods, data)
+        return ods