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Python routines to work with space data, particularly with MMS data. Also some general plasma routines.

License: MIT License

Python 100.00%

space-physics python3

irfu-python's Introduction

pyRFU

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

The Python package pyrfu is a software based on the IRFU-MATLAB library to work with space data, particularly the Magnetospheric MultiScale (MMS) mission.

It is distributed under the open-source MIT license.

Quickstart

Installing pyrfu with pip (more details here):

$ python -m pip install pyrfu
# or
$ python -m pip install --user pyrfu

Import pyrfu.mms package with routines specific to work with the Magnetospheric Multiscale mission (MMS)

from pyrfu import mms

Setup path to MMS data

mms.db_init("/Volumes/mms")

Load magnetic field and ion bulk velocity data

tint = ["2019-09-14T07:54:00.000", "2019-09-14T08:11:00.000"]
b_gsm = mms.get_data("b_gsm_fgm_srvy_l2", tint, 1)
v_gse_i = mms.get_data("vi_gse_fpi_fast_l2", tint, 1)

Import pyrfu.pyrf package with generic routines

from pyrfu import pyrf

Transform ion bulk velocity to geocentric solar magnetospheric (GSM) coordinates

v_gsm_i = pyrf.cotrans(v_gse_i, "gse>gsm")

Import pyrfu.plot package with plotting routines

from pyrfu import plot

Plot time series of magnetic field and ion bulk velocity

import matplotlib.pyplot as plt

f, axs = plt.subplots(2, sharex="all")
plot.plot_line(axs[0], b_gsm)
axs[0].set_ylabel("$B~[\\mathrm{nT}]$")
axs[0].legend(["$B_{x}$", "$B_{y}$", "$B_{z}$"], ncol=4)

plot.plot_line(axs[1], v_gsm_i)
axs[1].set_ylabel("$V_i~[\\mathrm{km}~\\mathrm{s}^{-1}]$")
axs[1].legend(["$V_{ix}$", "$V_{iy}$", "$V_{iz}$"], ncol=4)

Documentation

Full documentation can be found on pyrfu.readthedocs.io

Examples

A list of examples is available here

Credits

This software was developed by Louis RICHARD ([email protected]) based on the IRFU-MATLAB library.

Acknowledgement

Please use the following to acknowledge use of pyrfu in your publications: Data analysis was performed using the pyrfu analysis package available at https://github.com/louis-richard/irfu-python

Additional Information

MMS Science Data Center: https://lasp.colorado.edu/mms/sdc/public/

MMS Datasets: https://lasp.colorado.edu/mms/sdc/public/datasets/

MMS - Goddard Space Flight Center: http://mms.gsfc.nasa.gov/

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irfu-python's Issues

mms_keys.json missing perp/parallel ion moments

The required entries to the table would be:

        "tperpi_fpi_brst_l2": {
            "dtype": "dis-moms",
            "cdf_name": "dis_tempperp_brst"
        },
        "tparai_fpi_brst_l2": {
            "dtype": "dis-moms",
            "cdf_name": "dis_temppara_brst"
        },

pyrfu/mms/make_model_vdf.py import error

within the file pyrfu/mms/make_model_vdf.py there is an error TypeError: 'module' object is not callable on line 104.

I believe this is because on line 15 you are importing the module not the function within that module. When I changed line 15 to from .rotate_tensor import rotate_tensor it fixed the problem.

Problems using mms.get_data() without restarting Kernel

Hi Louis,

I created a new virtual environment to demonstrate this issue. I'm having it on my work copy of pyrfu (2.4.1) as well as the latest version which I installed today. The problem occurs when using get_data() on local files when it has not been downloaded in the same kernel run. It throws out an exception: AttributeError: 'NoneType' object has no attribute 'items'.

Downloading the data to a local file then loading it in (1 cell in jupyter notebook)

from pyrfu import mms

data_path = "D://MMS"
mms.db_init(data_path)

tint = ["2017-07-11T22:33:00.000", "2017-07-11T22:34:00.000"]

mms.download_data("pdi_fpi_brst_l2", tint, 1, data_path=data_path)
result = mms.get_data("pdi_fpi_brst_l2", tint, 1, data_path=data_path)

In another cell of the same Jupyter notebook, without restarting Kernel or re-downloading:

result = mms.get_data("pdi_fpi_brst_l2", tint, 1, data_path=data_path)

Throws the AttributeError exception.

I have this issue on most of my data intervals, but some do work. Another member in my department has the same problem on her installation, even when not using previously-downloaded data.

The full error is:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[2], [line 1](vscode-notebook-cell:?execution_count=2&line=1)
----> [1](vscode-notebook-cell:?execution_count=2&line=1) result = mms.get_data("pdi_fpi_brst_l2", tint, 1, data_path=data_path)

File [d:\Anaconda\envs\helpingcara\lib\site-packages\pyrfu\mms\get_data.py:126], in get_data(var_str, tint, mms_id, verbose, data_path, from_sdc)
    [123] file = os.path.normpath(file_name)
    [125] if "-dist" in var["dtype"]:
--> [126]     out = dist_append(out, get_dist(file, cdf_name, tint))
    [128] else:
    [129]     out = ts_append(out, get_ts(file, cdf_name, tint))

File [d:\Anaconda\envs\helpingcara\lib\site-packages\pyrfu\mms\get_dist.py:88] in get_dist(file_path, cdf_name, tint)
     [84]file = load(file_path)
     [86]# with CDF(file_path) as file:
     [87]# Get the relevant CDF file information (zVariables)
---> [88]z_vars = [z_var[0] for z_var in file.items()]
     [90]# Get the global attributes
     [91] glob_attrs = _pycdfpp_attributes_to_dict(file.attributes)

AttributeError: 'NoneType' object has no attribute 'items'

Enable reading data from SDC for MMS's FEEPS, EIS and remove_edist_background routines

The following routines read data only with local directory resources:

Compatibility with MMS SDC should be enabled.

Some Question

Hi, when I use the mms.psd_moments function, (I'm using the example you gave) I always get the following error: Traceback (most recent call last).
File "C:\Users\eric\AppData\Roaming\JetBrains\PyCharmCE2023.1\scratches\demo6.py", line 585, in
moments_e = mms.psd_moments(vdf_e, scpot, **options)
File "C:\anaconda\envs\pyrfu\lib\site-packages\pyrfu\mms\psd_moments.py", line 251, in psd_moments
field_name = vdf.attrs["FIELDNAM"]
KeyError: 'FIELDNAM'

from pyrfu import mms

tint_brst = ["2015-09-01T12:15:28.000", "2015-09-01T12:24:00.000"]

mms.download_data('pdi_fpi_brst_l2',tint_brst,1,data_path="C:\MMS\volumes")
scpot = mms.get_data("V_edp_brst_l2", tint_brst, 1)
vdf_e = mms.get_data("pde_fpi_brst_l2", tint_brst, 1)
options = dict(energy_range=[1, 1000])
moments_e = mms.psd_moments(vdf_e, scpot, **options)

How to set the database of MMS?

Dear Louis Richard,

      I do not know how to set the path of MMS database of pyrfu. 
   for example, in irf-matlab-master, we have to type: 
                        mms.db_init (' local_file_db ', path of database);
    But I do not know how to do it in this python code

thanks a lot!

Fix pandas read_csv depreciation warning

In pyrfu.mms.load_ancillary.py
FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use sep='\s+' instead

metadata-generation-failed when installing Pyrfu 2.4.12 to a conda environment

Hi Louis,

I created a new environment to install the latest pyrfu version, and I encounter an error with metadata generation during installation of the package dependencies. I do not encounter the problem for pyrfu version 2.4.11.

I am using pip to install the pyrfu package on a fresh conda environment (version 22.9.0). It seems as though this might be an error with the pycdfpp package?

I am not an expert in these things so I thought I would bring this to your attention in case any of this is within your control.

Collecting pycdfpp==0.6.0 (from pyrfu)
  Using cached pycdfpp-0.6.0.tar.gz (1.2 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [22 lines of output]
      + meson setup /private/var/folders/w1/vm9pp8qn443d01jr2j6tw41r0000gp/T/pip-install-zl9wk08i/pycdfpp_dd5575d2677f45aea33b2dd730546a9a /private/var/folders/w1/vm9pp8qn443d01jr2j6tw41r0000gp/T/pip-install-zl9wk08i/pycdfpp_dd5575d2677f45aea33b2dd730546a9a/.mesonpy-639kkxhx -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md -Doptimization=3 --native-file=/private/var/folders/w1/vm9pp8qn443d01jr2j6tw41r0000gp/T/pip-install-zl9wk08i/pycdfpp_dd5575d2677f45aea33b2dd730546a9a/.mesonpy-639kkxhx/meson-python-native-file.ini
      WARNING: Recommend using either -Dbuildtype or -Doptimization + -Ddebug. Using both is redundant since they override each other. See: https://mesonbuild.com/Builtin-options.html#build-type-options
      The Meson build system
      Version: 1.4.0
      Source dir: /private/var/folders/w1/vm9pp8qn443d01jr2j6tw41r0000gp/T/pip-install-zl9wk08i/pycdfpp_dd5575d2677f45aea33b2dd730546a9a
      Build dir: /private/var/folders/w1/vm9pp8qn443d01jr2j6tw41r0000gp/T/pip-install-zl9wk08i/pycdfpp_dd5575d2677f45aea33b2dd730546a9a/.mesonpy-639kkxhx
      Build type: native build
      WARNING: You should add the boolean check kwarg to the run_command call.
               It currently defaults to false,
               but it will default to true in future releases of meson.
               See also: https://github.com/mesonbuild/meson/issues/9300
      Project name: pycdfpp
      Project version: 0.6.0
      
      ../meson.build:1:0: ERROR: Unknown compiler(s): [['cc'], ['gcc'], ['clang'], ['nvc'], ['pgcc'], ['icc'], ['icx']]
      The following exception(s) were encountered:
      Running `nvc --version` gave "[Errno 2] No such file or directory: 'nvc'"
      Running `pgcc --version` gave "[Errno 2] No such file or directory: 'pgcc'"
      Running `icc --version` gave "[Errno 2] No such file or directory: 'icc'"
      Running `icx --version` gave "[Errno 2] No such file or directory: 'icx'"
      
      A full log can be found at /private/var/folders/w1/vm9pp8qn443d01jr2j6tw41r0000gp/T/pip-install-zl9wk08i/pycdfpp_dd5575d2677f45aea33b2dd730546a9a/.mesonpy-639kkxhx/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.

I hope this helps,
Harry

Update requirements to numba 0.59.0

Update requirements with numba>=0.59.0 to support Python>=3.9,<=3.12 https://numba.readthedocs.io/en/stable/release/0.59.0-notes.html

plot_projection() is unable to plot VDFs where energy bins are equivalent to less than the spacecraft potential

The problem seems to come from the vdf_projection function, which is taking the square root of shifted energy bins. When the bins are smaller than the spacecraft potential, they are shifted to negative numbers and the np.sqrt() function is returning nan. The pcolormesh function can't accept nans as bin coordinates, which causes an error in plot_projection.py.

To fix this, I suggest np.sqrt(..., dtype=np.csingle) or np.emath.sqrt(...) on line 348 of vdf_projection.py.

Doing this gives 0 for the "negative" velocity bins, which I believe to be your intention based on the np.real() function on line 349. However, it might not be the perfect solution as it stretches the innermost bin to the center of the polar plot.

If you need an example timestep, use 1475257837.6974614 a.k.a ['2016-09-30T17:50:37.697'].

Running on pyrfu version 2.4.12 but with dependencies installed for 2.4.11 (see my other issue).

Hope this helps.