Export to ‘.tmat.h5’ format with Python

Author

baptiste, with inital code from Nigar

Published

June 27, 2024

This document showcases a basic Matlab script to export T-matrices in the .tmat.h5 HDF5 format. For illustration, we start by producing a dummy dataset. This minimal reproducible example file is available for download as a standalone script: export_python.py.

Mockup input data

Consistent with the other examples, we generate a 50x30x30 array of dummy data, which repeats 50 times (50 wavelengths) a matrix of 900 entries ranging from \(1+1i\) (first element, top left) to \(900 + 900i\) (last element, bottom right). Note the expectation of row-major ordering in HDF5. The 3x3 top-left block is

   1.0000 + 1.0000i   2.0000 + 2.0000i   3.0000 + 3.0000i ...
  31.0000 +31.0000i  32.0000 +32.0000i  33.0000 +33.0000i ...
  61.0000 +61.0000i  62.0000 +62.0000i  63.0000 +63.0000i ...
   ...               ...                ...               ...

The Python library h5py provides a convenient object-oriented interface to save python objects in the required HDF5 structure, so we don’t need particular care to organise them on the Python side.

import numpy as np
import os, sys
import h5py
#possibly multiple wavelengths
wavelength  = np.arange(400,850, 50)
Nl = len(wavelength)
lmax = 3
qmax = 2*(lmax*(lmax+1)+lmax)
# dummy 30x30 matrix values repeated for each wavelength
tdata = np.reshape(np.arange(1,901,1) + 1j*np.arange(1,901,1), (qmax,qmax))
tmatrix = np.zeros((Nl,qmax,qmax), dtype="complex")
for i in range(Nl):
  tmatrix[i,:,:] = tdata

print(tmatrix[0,0:3,0:3])

l = np.zeros(qmax)
m = np.zeros(qmax)
s = np.array([b'xxxxxxic']*len(l))
i=0
for li in range(1,lmax+1):
    for mi in range(-li, li+1):
        for si in [b'electric', b'magnetic']:
            l[i] = li
            m[i] = mi
            s[i] = si
            i = i+1

Saving to HDF5

The Python library h5py provides a convenient interface to generate groups, datasets, and attributes with simple assigments:

# Saving to HDF5
f = 'ap.tmat.h5';
with h5py.File(f, "w") as f:
    f["vacuum_wavelength"] = np.asarray(wavelength)
    f["vacuum_wavelength"].attrs["unit"] = "nm"
    f["tmatrix"] = tmatrix
    f['modes/l'] = l
    f['modes/m'] = m
    f['modes/polarization'] = s
    emb = f.create_group(f"embedding")
    emb["relative_permittivity"] = 1.33**2
    emb["relative_permeability"] = 1.0
    emb.attrs["name"] = "H2O, Water"
    emb.attrs["keywords"] = "non-dispersive"
    sca_mat = f.create_group("scatterer/material")
    sca_mat.attrs["name"] = 'Au, Gold'
    sca_mat.attrs["keywords"] = "dispersive, plasmonic"
    sca_mat.attrs["reference"] = "Au from Raschke et al 10.1103/PhysRevB.86.235147"
    sca_mat["relative_permittivity"] = np.ones(len(wavelength), dtype = complex)*(-11.4+1.181j)
    sca_mat["relative_permeability"] = 1.0
    sca_gr = f.create_group("scatterer/geometry")
    sca_gr["radiusxy"] = 20.0
    sca_gr["radiusz"] = 40.0
    sca_gr.attrs['unit'] = 'nm'
    sca_gr.attrs['shape'] = 'spheroid'
    sca_gr.attrs['name'] = 'homogeneous spheroid with symmetry axis z'
    mpar = f.create_group("computation/method_parameters")
    #f["computation/analytical_zeros"] = analytical_zeros # not needed in this example
    mpar["Lmax"] = lmax
    mpar["Ntheta"] = 100
    f.create_group("computation/files")
    with open(__file__, "r") as scriptfile:
        f[f"computation/files/{os.path.basename(__file__)}"] = scriptfile.read()
    f["computation"].attrs["method"] = "EBCM, Extended Boundary Condition Method" 
    f["computation"].attrs["description"] = "Computation using SMARTIES, a numerically robust EBCM implementation for spheroids" 
    f["computation"].attrs["software"] = f"SMARTIES=1.1, python={sys.version.split()[0]}, h5py={h5py.__version__}"
    f["computation"].attrs["name"] = "SMARTIES"
    f.attrs['name'] = 'Au prolate spheroid in water'
    f.attrs['keywords'] = 'gold, spheroid, ebcm, passive, reciprocal, czinfinity, mirrorxyz'
    f.attrs['description'] = 'Computation using SMARTIES, a numerically robust EBCM implementation for spheroids'
    f.attrs['storage_format_version'] = 'v0.01'

Summary of the file:

<list>
├─data: <list>
│ ├─computation: <list>
│ │ ├─files: <list>
│ │ │ └─export_python.py: "import numpy as np↵import os, sy..."
│ │ └─method_parameters: <list>
│ │   ├─Lmax: 3
│ │   └─Ntheta: 100
│ ├─embedding: <list>
│ │ ├─relative_permeability: 1
│ │ └─relative_permittivity: 1.7689
│ ├─modes: <list>
│ │ ├─l<dbl [30]>: 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, ...
│ │ ├─m<dbl [30]>: -1, -1, 0, 0, 1, 1, -2, -2, -1, -1, ...
│ │ └─polarization<chr [30]>: "electric", "magnetic", "electric", "magnetic", "electric", "magnetic", "electric", "magnetic", "electric", "magnetic", ...
│ ├─scatterer: <list>
│ │ ├─geometry: <list>
│ │ │ ├─radiusxy: 20
│ │ │ └─radiusz: 40
│ │ └─material: <list>
│ │   ├─relative_permeability: 1
│ │   └─relative_permittivity<cpl [9]>: -11.4+1.181i, -11.4+1.181i, -11.4+1.181i, -11.4+1.181i, -11.4+1.181i, -11.4+1.181i, -11.4+1.181i, -11.4+1.181i, -11.4+1.181i
│ ├─tmatrix<cpl [8,100]>: 1+1i, 1+1i, 1+1i, 1+1i, 1+1i, 1+1i, 1+1i, 1+1i, 1+1i, 31+31i, ...
│ └─vacuum_wavelength<int [9]>: 400, 450, 500, 550, 600, 650, 700, 750, 800
└─attributes: <list>
  ├─root: <list>
  │ ├─description: "Computation using SMARTIES, a nu..."
  │ ├─keywords: "gold, spheroid, ebcm, passive, r..."
  │ ├─name: "Au prolate spheroid in water"
  │ └─storage_format_version: "v0.01"
  ├─vacuum_wavelength: <list>
  │ └─unit: "nm"
  ├─computation: <list>
  │ ├─description: "Computation using SMARTIES, a nu..."
  │ ├─method: "EBCM, Extended Boundary Conditio..."
  │ ├─name: "SMARTIES"
  │ └─software: "SMARTIES=1.1, python=3.11.7, h5p..."
  ├─embedding: <list>
  │ ├─keywords: "non-dispersive"
  │ └─name: "H2O, Water"
  ├─material: <list>
  │ ├─keywords: "dispersive, plasmonic"
  │ ├─name: "Au, Gold"
  │ └─reference: "Au from Raschke et al 10.1103/Ph..."
  └─geometry: <list>
    ├─name: "homogeneous spheroid with symmet..."
    ├─shape: "spheroid"
    └─unit: "nm"