quant-aq / py-smps Goto Github PK

Python library for the analysis and visualization of data from a Scanning Mobility Particle Sizer (SMPS) and other similar instruments (SEMS, OPC's).

Home Page: https://quant-aq.github.io/py-smps/

License: MIT License

Python 100.00%

science aerosol mit chemistry atmospheric-science

py-smps's People

Contributors

Stargazers

Watchers

Forkers

duanyscn gorkowski haochiche ilir-shuli moabgal pure-alone benjistomps linlin12333 rxward persisli haniehkhoshnevisansari lfyin verafirmansyah

py-smps's Issues

Add results class for returning fitted data

look at statsmodels for inspiration (for tables)

Build Interactive Exploration tool based on plotly

https://plot.ly/javascript/lasso-selection/

Warning with histogram plots

Error in installation of py-smps using pip. It finishes with error. Do you have any suggestions what could be the reason for this.

C:\Users\au748849>pip install py-smps
Collecting py-smps
Using cached py_smps-2.0.0-py3-none-any.whl (19 kB)
Collecting joblib<2.0.0,>=1.0.0 (from py-smps)
Using cached joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting numpy<2.0.0,>=1.19.1 (from py-smps)
Using cached numpy-1.26.3-cp312-cp312-win_amd64.whl.metadata (61 kB)
Collecting pandas<2.0.0,>=1.2.4 (from py-smps)
Using cached pandas-1.5.3.tar.gz (5.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting requests<3.0.0,>=2.24.0 (from py-smps)
Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting scipy<2.0.0,>=1.5.2 (from py-smps)
Using cached scipy-1.11.4-cp312-cp312-win_amd64.whl.metadata (60 kB)
Collecting seaborn<0.11.0,>=0.10.1 (from py-smps)
Using cached seaborn-0.10.1-py3-none-any.whl (215 kB)
Collecting statsmodels<0.13.0,>=0.12.0 (from py-smps)
Using cached statsmodels-0.12.2.tar.gz (17.5 MB)
Installing build dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [297 lines of output]
Ignoring numpy: markers 'python_version == "3.6"' don't match your environment
Ignoring numpy: markers 'python_version == "3.7"' don't match your environment
Collecting setuptools
Using cached setuptools-69.0.3-py3-none-any.whl.metadata (6.3 kB)
Collecting wheel
Using cached wheel-0.42.0-py3-none-any.whl.metadata (2.2 kB)
Collecting cython>=0.29.14
Using cached Cython-3.0.8-cp312-cp312-win_amd64.whl.metadata (3.2 kB)
Collecting numpy==1.17.5
Using cached numpy-1.17.5.zip (6.4 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error

    Preparing metadata (pyproject.toml) did not run successfully.
    exit code: 1

    [264 lines of output]
    Running from numpy source directory.
    <string>:419: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
    blas_opt_info:
    blas_mkl_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries mkl_rt not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    blis_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries blis not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    openblas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries openblas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
    get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
    customize GnuFCompiler
    Could not locate executable g77
    Could not locate executable f77
    customize IntelVisualFCompiler
    Could not locate executable ifort
    Could not locate executable ifl
    customize AbsoftFCompiler
    Could not locate executable f90
    customize CompaqVisualFCompiler
    Could not locate executable DF
    customize IntelItaniumVisualFCompiler
    Could not locate executable efl
    customize Gnu95FCompiler
    Could not locate executable gfortran
    Could not locate executable f95
    customize G95FCompiler
    Could not locate executable g95
    customize IntelEM64VisualFCompiler
    customize IntelEM64TFCompiler
    Could not locate executable efort
    Could not locate executable efc
    customize PGroupFlangCompiler
    Could not locate executable flang
    don't know how to compile Fortran code on platform 'nt'
      NOT AVAILABLE

    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    atlas_3_10_blas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    atlas_blas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    accelerate_info:
      NOT AVAILABLE

    C:\Users\au748849\AppData\Local\Temp\pip-install-ccccaoze\numpy_22164a338e2a440cad5670d7f62254be\numpy\distutils\system_info.py:690: UserWarning:
        Optimized (vendor) Blas libraries are not found.
        Falls back to netlib Blas library which has worse performance.
        A better performance should be easily gained by switching
        Blas library.
      self.calc_info()
    blas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries blas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    C:\Users\au748849\AppData\Local\Temp\pip-install-ccccaoze\numpy_22164a338e2a440cad5670d7f62254be\numpy\distutils\system_info.py:690: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      self.calc_info()
    blas_src_info:
      NOT AVAILABLE

    C:\Users\au748849\AppData\Local\Temp\pip-install-ccccaoze\numpy_22164a338e2a440cad5670d7f62254be\numpy\distutils\system_info.py:690: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE

    'svnversion' is not recognized as an internal or external command,
    operable program or batch file.
    non-existing path in 'numpy\\distutils': 'site.cfg'
    lapack_opt_info:
    lapack_mkl_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries mkl_rt not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    openblas_lapack_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries openblas not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    openblas_clapack_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries openblas,lapack not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    flame_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries flame not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas,tatlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas,tatlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries tatlas,tatlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas,satlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas,satlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries satlas,satlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries ptf77blas,ptcblas,atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\lib
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in C:\
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack_atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries f77blas,cblas,atlas not found in C:\Users\au748849\AppData\Local\Programs\Python\Python312\libs
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    lapack_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries lapack not found in ['C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\lib', 'C:\\', 'C:\\Users\\au748849\\AppData\\Local\\Programs\\Python\\Python312\\libs']
      NOT AVAILABLE

    C:\Users\au748849\AppData\Local\Temp\pip-install-ccccaoze\numpy_22164a338e2a440cad5670d7f62254be\numpy\distutils\system_info.py:1712: UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      if getattr(self, '_calc_info_{}'.format(lapack))():
    lapack_src_info:
      NOT AVAILABLE

    C:\Users\au748849\AppData\Local\Temp\pip-install-ccccaoze\numpy_22164a338e2a440cad5670d7f62254be\numpy\distutils\system_info.py:1712: UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      if getattr(self, '_calc_info_{}'.format(lapack))():
      NOT AVAILABLE

    C:\Users\au748849\AppData\Local\Temp\pip-build-env-tyt_f4uo\overlay\Lib\site-packages\setuptools\_distutils\dist.py:265: UserWarning: Unknown distribution option: 'define_macros'
      warnings.warn(msg)
    running dist_info
    running build_src
    build_src
    building py_modules sources
    creating build
    creating build\src.win-amd64-3.1
    creating build\src.win-amd64-3.1\numpy
    creating build\src.win-amd64-3.1\numpy\distutils
    building library "npymath" sources
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
    [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.
  hint: See above for details.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Add support for merging together multiple scans with different bins

Currently, bins is a 3xn array - if we turn it into a 3 x n x y array (i.e. all timestamps have a unique bin array), we can merge together files with different parameters.

OPC-N3 is missing a bin by default

Error when plotting smps.plots.heatmap

Discussed in #51

^{Originally posted by Ethan-Barber July 25, 2022}
When I copy the code for the sample "boston" example and plot the heatmap, I receive the error "Cannot cast ufunc 'greater_equal' input 0 from dtype('<m8[ns]') to dtype('<m8') with casting rule 'same_kind'". Any ideas how I can fix this?

Curve Fitting

Support multi-modal curve fititng

The OPCN2/N3 Loader sucks

Should be more generic since Alphasense just changed the output format in their new GUI

Make accessing GM, GSD, other stats easier

Throw more useful errors

Specifically, on a failed file import, throw a more useful error.

Colormap Plot has blank areas where dNdlogDp is less than Z.min()

Should we somehow fix this heatmap so that any datapoint less than the LogNorm minimum appears visually as the minimum? i.e. If we set cbar_min=100, then any data point where dNdlogDp < 100 will appear white, rather than the minimum colorbar color..

smps.plots.heatmap error

Describe the bug
UFuncTypeError when using smps.plots.heatmap example

To Reproduce
Steps to reproduce the behavior:

import "Boston" example
copy example code for Boston example to produce heatmap
Receive error shown below

Expected behavior
Produces error:

"Cannot cast ufunc 'greater_equal' input 0 from dtype('<m8[ns]') to dtype('<m8') with casting rule 'same_kind'"
heatmap plot will not display.

Screenshots
heatmaperror.pdf

Desktop (please complete the following information):

OS: [ macOS Monterey]
Browser [Chrom]
Version [104.0.5112.79]

Additional context
Add any other context about the problem here.

The requirement for `setuptools` should be loosened if possible

Describe the bug
When installing py-smps, the dependency for setuptools is quite strict, which can lead to issues for users. If the proper version of setuptools is installed, everything is fine. If not, it raises the exception below:

To Reproduce
Steps to reproduce the behavior:

Install py-smps with setuptools<65.0
Try to use py-smps

Expected behavior
The package should work independent of setuptools version

Python Environment (please complete the following information)

python3.9

Port this library over to QuantAQ

This library will be supported by QuantAQ from now on and will live under the QuantAQ GitHub umbrella.

heatmap should more intelligently deal with non-positive numbers

Specifically, 0's and NaNs throws a ValueError

Problems when there are empty spots in the dataframe

It would be nice if we could plot the heatmap while leaving missing rows alone.

Add existing contributors to the README

Calculate Relevant Params

We should be able to do the following:

Calculate mean, mode, etc
Fit data to n lognormal modes
convert between number-weighted, surface-weighted, etc.

Add 'mode' to the stats

Outdated smps.io.load_file() in tutorial

The "smps.io.load_file" method is supposed to be "smps_from_txt" in the tutorial.

Add .copy() method to SMPS class

Error tokenizing data

Hi,
thank you very much for this library, I get the following error when trying to open a new SMPS file:

CParserError: Error tokenizing data. C error: Expected 3 fields in line 3, saw 6

Please note that I'm using the following command: smps.io.load_file(fpath, column=False)
Moreover, I'm working with Python 2.7, maybe this is the problem....

Thank you,
Andrea

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
py-smps 2.0.0 requires seaborn<0.11.0,>=0.10.1, but you have seaborn 0.11.2 which is incompatible.

Alphasense OPC-N3 object is not being initiated correctly

If you do not specify the bin_labels, the bin labels are not auto-generated as they should. Code here

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