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- .gitattributes +16 -0
- videochat2/lib/python3.10/site-packages/scipy/constants/__pycache__/_codata.cpython-310.pyc +3 -0
- videochat2/lib/python3.10/site-packages/scipy/io/__init__.py +116 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_fortran.py +354 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__init__.py +17 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__pycache__/__init__.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__pycache__/_fortran_format_parser.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__pycache__/hb.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/_fortran_format_parser.py +309 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/hb.py +571 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__init__.py +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__pycache__/__init__.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__pycache__/test_fortran_format.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__pycache__/test_hb.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/test_fortran_format.py +74 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/test_hb.py +65 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_idl.py +918 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_mmio.py +961 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_netcdf.py +1095 -0
- videochat2/lib/python3.10/site-packages/scipy/io/_test_fortran.cpython-310-x86_64-linux-gnu.so +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/harwell_boeing.py +21 -0
- videochat2/lib/python3.10/site-packages/scipy/io/idl.py +20 -0
- videochat2/lib/python3.10/site-packages/scipy/io/mmio.py +20 -0
- videochat2/lib/python3.10/site-packages/scipy/io/netcdf.py +25 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__init__.py +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/__init__.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/test_fortran.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/test_idl.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/test_mmio.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/test_netcdf.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/test_paths.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/test_wavfile.cpython-310.pyc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/array_float32_1d.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/array_float32_3d.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/array_float32_pointer_3d.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/array_float32_pointer_4d.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/array_float32_pointer_7d.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/example_3_maskedvals.nc +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/fortran-mixed.dat +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/fortran-sf8-1x1x1.dat +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/fortran-sf8-1x3x5.dat +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/fortran-si4-1x1x7.dat +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/invalid_pointer.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/scalar_complex32.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/scalar_int32.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/scalar_int64.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/scalar_uint32.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/struct_arrays_replicated.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/struct_pointer_arrays.sav +0 -0
- videochat2/lib/python3.10/site-packages/scipy/io/tests/data/struct_pointer_arrays_replicated.sav +0 -0
.gitattributes
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videochat2/lib/python3.10/site-packages/av/error.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/av/audio/frame.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/av/error.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/av/audio/frame.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/av/container/pyio.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/constants/__pycache__/_codata.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_rcont/rcont.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_unuran/unuran_wrapper.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/ncx2_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/tests/__pycache__/test_multivariate.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/beta_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/tests/__pycache__/test_stats.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/ncf_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/skewnorm_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/__pycache__/_distn_infrastructure.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/nbinom_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/tests/__pycache__/test_distributions.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/nct_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/hypergeom_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/invgauss_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/stats/_boost/binom_ufunc.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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videochat2/lib/python3.10/site-packages/scipy/constants/__pycache__/_codata.cpython-310.pyc
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version https://git-lfs.github.com/spec/v1
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oid sha256:30da37d7bcb69e837a546d4023e15680393266f49120253f3c4138fc1adb527c
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size 153730
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videochat2/lib/python3.10/site-packages/scipy/io/__init__.py
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"""
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==================================
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Input and output (:mod:`scipy.io`)
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==================================
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| 5 |
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| 6 |
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.. currentmodule:: scipy.io
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| 7 |
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| 8 |
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SciPy has many modules, classes, and functions available to read data
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from and write data to a variety of file formats.
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| 10 |
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| 11 |
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.. seealso:: `NumPy IO routines <https://www.numpy.org/devdocs/reference/routines.io.html>`__
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| 12 |
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MATLAB® files
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| 14 |
+
=============
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| 15 |
+
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| 16 |
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.. autosummary::
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| 17 |
+
:toctree: generated/
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| 18 |
+
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| 19 |
+
loadmat - Read a MATLAB style mat file (version 4 through 7.1)
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| 20 |
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savemat - Write a MATLAB style mat file (version 4 through 7.1)
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| 21 |
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whosmat - List contents of a MATLAB style mat file (version 4 through 7.1)
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| 22 |
+
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| 23 |
+
For low-level MATLAB reading and writing utilities, see `scipy.io.matlab`.
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| 24 |
+
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| 25 |
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IDL® files
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| 26 |
+
==========
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| 27 |
+
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| 28 |
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.. autosummary::
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| 29 |
+
:toctree: generated/
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| 30 |
+
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| 31 |
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readsav - Read an IDL 'save' file
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| 32 |
+
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| 33 |
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Matrix Market files
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| 34 |
+
===================
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| 35 |
+
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| 36 |
+
.. autosummary::
|
| 37 |
+
:toctree: generated/
|
| 38 |
+
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| 39 |
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mminfo - Query matrix info from Matrix Market formatted file
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| 40 |
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mmread - Read matrix from Matrix Market formatted file
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| 41 |
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mmwrite - Write matrix to Matrix Market formatted file
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| 42 |
+
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| 43 |
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Unformatted Fortran files
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| 44 |
+
===============================
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| 45 |
+
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| 46 |
+
.. autosummary::
|
| 47 |
+
:toctree: generated/
|
| 48 |
+
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| 49 |
+
FortranFile - A file object for unformatted sequential Fortran files
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| 50 |
+
FortranEOFError - Exception indicating the end of a well-formed file
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| 51 |
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FortranFormattingError - Exception indicating an inappropriate end
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| 52 |
+
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| 53 |
+
Netcdf
|
| 54 |
+
======
|
| 55 |
+
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| 56 |
+
.. autosummary::
|
| 57 |
+
:toctree: generated/
|
| 58 |
+
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| 59 |
+
netcdf_file - A file object for NetCDF data
|
| 60 |
+
netcdf_variable - A data object for the netcdf module
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| 61 |
+
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| 62 |
+
Harwell-Boeing files
|
| 63 |
+
====================
|
| 64 |
+
|
| 65 |
+
.. autosummary::
|
| 66 |
+
:toctree: generated/
|
| 67 |
+
|
| 68 |
+
hb_read -- read H-B file
|
| 69 |
+
hb_write -- write H-B file
|
| 70 |
+
|
| 71 |
+
Wav sound files (:mod:`scipy.io.wavfile`)
|
| 72 |
+
=========================================
|
| 73 |
+
|
| 74 |
+
.. module:: scipy.io.wavfile
|
| 75 |
+
|
| 76 |
+
.. autosummary::
|
| 77 |
+
:toctree: generated/
|
| 78 |
+
|
| 79 |
+
read
|
| 80 |
+
write
|
| 81 |
+
WavFileWarning
|
| 82 |
+
|
| 83 |
+
Arff files (:mod:`scipy.io.arff`)
|
| 84 |
+
=================================
|
| 85 |
+
|
| 86 |
+
.. module:: scipy.io.arff
|
| 87 |
+
|
| 88 |
+
.. autosummary::
|
| 89 |
+
:toctree: generated/
|
| 90 |
+
|
| 91 |
+
loadarff
|
| 92 |
+
MetaData
|
| 93 |
+
ArffError
|
| 94 |
+
ParseArffError
|
| 95 |
+
"""
|
| 96 |
+
# matfile read and write
|
| 97 |
+
from .matlab import loadmat, savemat, whosmat
|
| 98 |
+
|
| 99 |
+
# netCDF file support
|
| 100 |
+
from ._netcdf import netcdf_file, netcdf_variable
|
| 101 |
+
|
| 102 |
+
# Fortran file support
|
| 103 |
+
from ._fortran import FortranFile, FortranEOFError, FortranFormattingError
|
| 104 |
+
|
| 105 |
+
from ._fast_matrix_market import mminfo, mmread, mmwrite
|
| 106 |
+
from ._idl import readsav
|
| 107 |
+
from ._harwell_boeing import hb_read, hb_write
|
| 108 |
+
|
| 109 |
+
# Deprecated namespaces, to be removed in v2.0.0
|
| 110 |
+
from . import arff, harwell_boeing, idl, mmio, netcdf, wavfile
|
| 111 |
+
|
| 112 |
+
__all__ = [s for s in dir() if not s.startswith('_')]
|
| 113 |
+
|
| 114 |
+
from scipy._lib._testutils import PytestTester
|
| 115 |
+
test = PytestTester(__name__)
|
| 116 |
+
del PytestTester
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videochat2/lib/python3.10/site-packages/scipy/io/_fortran.py
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|
| 1 |
+
"""
|
| 2 |
+
Module to read / write Fortran unformatted sequential files.
|
| 3 |
+
|
| 4 |
+
This is in the spirit of code written by Neil Martinsen-Burrell and Joe Zuntz.
|
| 5 |
+
|
| 6 |
+
"""
|
| 7 |
+
import warnings
|
| 8 |
+
import numpy as np
|
| 9 |
+
|
| 10 |
+
__all__ = ['FortranFile', 'FortranEOFError', 'FortranFormattingError']
|
| 11 |
+
|
| 12 |
+
|
| 13 |
+
class FortranEOFError(TypeError, OSError):
|
| 14 |
+
"""Indicates that the file ended properly.
|
| 15 |
+
|
| 16 |
+
This error descends from TypeError because the code used to raise
|
| 17 |
+
TypeError (and this was the only way to know that the file had
|
| 18 |
+
ended) so users might have ``except TypeError:``.
|
| 19 |
+
|
| 20 |
+
"""
|
| 21 |
+
pass
|
| 22 |
+
|
| 23 |
+
|
| 24 |
+
class FortranFormattingError(TypeError, OSError):
|
| 25 |
+
"""Indicates that the file ended mid-record.
|
| 26 |
+
|
| 27 |
+
Descends from TypeError for backward compatibility.
|
| 28 |
+
|
| 29 |
+
"""
|
| 30 |
+
pass
|
| 31 |
+
|
| 32 |
+
|
| 33 |
+
class FortranFile:
|
| 34 |
+
"""
|
| 35 |
+
A file object for unformatted sequential files from Fortran code.
|
| 36 |
+
|
| 37 |
+
Parameters
|
| 38 |
+
----------
|
| 39 |
+
filename : file or str
|
| 40 |
+
Open file object or filename.
|
| 41 |
+
mode : {'r', 'w'}, optional
|
| 42 |
+
Read-write mode, default is 'r'.
|
| 43 |
+
header_dtype : dtype, optional
|
| 44 |
+
Data type of the header. Size and endianness must match the input/output file.
|
| 45 |
+
|
| 46 |
+
Notes
|
| 47 |
+
-----
|
| 48 |
+
These files are broken up into records of unspecified types. The size of
|
| 49 |
+
each record is given at the start (although the size of this header is not
|
| 50 |
+
standard) and the data is written onto disk without any formatting. Fortran
|
| 51 |
+
compilers supporting the BACKSPACE statement will write a second copy of
|
| 52 |
+
the size to facilitate backwards seeking.
|
| 53 |
+
|
| 54 |
+
This class only supports files written with both sizes for the record.
|
| 55 |
+
It also does not support the subrecords used in Intel and gfortran compilers
|
| 56 |
+
for records which are greater than 2GB with a 4-byte header.
|
| 57 |
+
|
| 58 |
+
An example of an unformatted sequential file in Fortran would be written as::
|
| 59 |
+
|
| 60 |
+
OPEN(1, FILE=myfilename, FORM='unformatted')
|
| 61 |
+
|
| 62 |
+
WRITE(1) myvariable
|
| 63 |
+
|
| 64 |
+
Since this is a non-standard file format, whose contents depend on the
|
| 65 |
+
compiler and the endianness of the machine, caution is advised. Files from
|
| 66 |
+
gfortran 4.8.0 and gfortran 4.1.2 on x86_64 are known to work.
|
| 67 |
+
|
| 68 |
+
Consider using Fortran direct-access files or files from the newer Stream
|
| 69 |
+
I/O, which can be easily read by `numpy.fromfile`.
|
| 70 |
+
|
| 71 |
+
Examples
|
| 72 |
+
--------
|
| 73 |
+
To create an unformatted sequential Fortran file:
|
| 74 |
+
|
| 75 |
+
>>> from scipy.io import FortranFile
|
| 76 |
+
>>> import numpy as np
|
| 77 |
+
>>> f = FortranFile('test.unf', 'w')
|
| 78 |
+
>>> f.write_record(np.array([1,2,3,4,5], dtype=np.int32))
|
| 79 |
+
>>> f.write_record(np.linspace(0,1,20).reshape((5,4)).T)
|
| 80 |
+
>>> f.close()
|
| 81 |
+
|
| 82 |
+
To read this file:
|
| 83 |
+
|
| 84 |
+
>>> f = FortranFile('test.unf', 'r')
|
| 85 |
+
>>> print(f.read_ints(np.int32))
|
| 86 |
+
[1 2 3 4 5]
|
| 87 |
+
>>> print(f.read_reals(float).reshape((5,4), order="F"))
|
| 88 |
+
[[0. 0.05263158 0.10526316 0.15789474]
|
| 89 |
+
[0.21052632 0.26315789 0.31578947 0.36842105]
|
| 90 |
+
[0.42105263 0.47368421 0.52631579 0.57894737]
|
| 91 |
+
[0.63157895 0.68421053 0.73684211 0.78947368]
|
| 92 |
+
[0.84210526 0.89473684 0.94736842 1. ]]
|
| 93 |
+
>>> f.close()
|
| 94 |
+
|
| 95 |
+
Or, in Fortran::
|
| 96 |
+
|
| 97 |
+
integer :: a(5), i
|
| 98 |
+
double precision :: b(5,4)
|
| 99 |
+
open(1, file='test.unf', form='unformatted')
|
| 100 |
+
read(1) a
|
| 101 |
+
read(1) b
|
| 102 |
+
close(1)
|
| 103 |
+
write(*,*) a
|
| 104 |
+
do i = 1, 5
|
| 105 |
+
write(*,*) b(i,:)
|
| 106 |
+
end do
|
| 107 |
+
|
| 108 |
+
"""
|
| 109 |
+
def __init__(self, filename, mode='r', header_dtype=np.uint32):
|
| 110 |
+
if header_dtype is None:
|
| 111 |
+
raise ValueError('Must specify dtype')
|
| 112 |
+
|
| 113 |
+
header_dtype = np.dtype(header_dtype)
|
| 114 |
+
if header_dtype.kind != 'u':
|
| 115 |
+
warnings.warn("Given a dtype which is not unsigned.", stacklevel=2)
|
| 116 |
+
|
| 117 |
+
if mode not in 'rw' or len(mode) != 1:
|
| 118 |
+
raise ValueError('mode must be either r or w')
|
| 119 |
+
|
| 120 |
+
if hasattr(filename, 'seek'):
|
| 121 |
+
self._fp = filename
|
| 122 |
+
else:
|
| 123 |
+
self._fp = open(filename, '%sb' % mode)
|
| 124 |
+
|
| 125 |
+
self._header_dtype = header_dtype
|
| 126 |
+
|
| 127 |
+
def _read_size(self, eof_ok=False):
|
| 128 |
+
n = self._header_dtype.itemsize
|
| 129 |
+
b = self._fp.read(n)
|
| 130 |
+
if (not b) and eof_ok:
|
| 131 |
+
raise FortranEOFError("End of file occurred at end of record")
|
| 132 |
+
elif len(b) < n:
|
| 133 |
+
raise FortranFormattingError(
|
| 134 |
+
"End of file in the middle of the record size")
|
| 135 |
+
return int(np.frombuffer(b, dtype=self._header_dtype, count=1)[0])
|
| 136 |
+
|
| 137 |
+
def write_record(self, *items):
|
| 138 |
+
"""
|
| 139 |
+
Write a record (including sizes) to the file.
|
| 140 |
+
|
| 141 |
+
Parameters
|
| 142 |
+
----------
|
| 143 |
+
*items : array_like
|
| 144 |
+
The data arrays to write.
|
| 145 |
+
|
| 146 |
+
Notes
|
| 147 |
+
-----
|
| 148 |
+
Writes data items to a file::
|
| 149 |
+
|
| 150 |
+
write_record(a.T, b.T, c.T, ...)
|
| 151 |
+
|
| 152 |
+
write(1) a, b, c, ...
|
| 153 |
+
|
| 154 |
+
Note that data in multidimensional arrays is written in
|
| 155 |
+
row-major order --- to make them read correctly by Fortran
|
| 156 |
+
programs, you need to transpose the arrays yourself when
|
| 157 |
+
writing them.
|
| 158 |
+
|
| 159 |
+
"""
|
| 160 |
+
items = tuple(np.asarray(item) for item in items)
|
| 161 |
+
total_size = sum(item.nbytes for item in items)
|
| 162 |
+
|
| 163 |
+
nb = np.array([total_size], dtype=self._header_dtype)
|
| 164 |
+
|
| 165 |
+
nb.tofile(self._fp)
|
| 166 |
+
for item in items:
|
| 167 |
+
item.tofile(self._fp)
|
| 168 |
+
nb.tofile(self._fp)
|
| 169 |
+
|
| 170 |
+
def read_record(self, *dtypes, **kwargs):
|
| 171 |
+
"""
|
| 172 |
+
Reads a record of a given type from the file.
|
| 173 |
+
|
| 174 |
+
Parameters
|
| 175 |
+
----------
|
| 176 |
+
*dtypes : dtypes, optional
|
| 177 |
+
Data type(s) specifying the size and endianness of the data.
|
| 178 |
+
|
| 179 |
+
Returns
|
| 180 |
+
-------
|
| 181 |
+
data : ndarray
|
| 182 |
+
A 1-D array object.
|
| 183 |
+
|
| 184 |
+
Raises
|
| 185 |
+
------
|
| 186 |
+
FortranEOFError
|
| 187 |
+
To signal that no further records are available
|
| 188 |
+
FortranFormattingError
|
| 189 |
+
To signal that the end of the file was encountered
|
| 190 |
+
part-way through a record
|
| 191 |
+
|
| 192 |
+
Notes
|
| 193 |
+
-----
|
| 194 |
+
If the record contains a multidimensional array, you can specify
|
| 195 |
+
the size in the dtype. For example::
|
| 196 |
+
|
| 197 |
+
INTEGER var(5,4)
|
| 198 |
+
|
| 199 |
+
can be read with::
|
| 200 |
+
|
| 201 |
+
read_record('(4,5)i4').T
|
| 202 |
+
|
| 203 |
+
Note that this function does **not** assume the file data is in Fortran
|
| 204 |
+
column major order, so you need to (i) swap the order of dimensions
|
| 205 |
+
when reading and (ii) transpose the resulting array.
|
| 206 |
+
|
| 207 |
+
Alternatively, you can read the data as a 1-D array and handle the
|
| 208 |
+
ordering yourself. For example::
|
| 209 |
+
|
| 210 |
+
read_record('i4').reshape(5, 4, order='F')
|
| 211 |
+
|
| 212 |
+
For records that contain several variables or mixed types (as opposed
|
| 213 |
+
to single scalar or array types), give them as separate arguments::
|
| 214 |
+
|
| 215 |
+
double precision :: a
|
| 216 |
+
integer :: b
|
| 217 |
+
write(1) a, b
|
| 218 |
+
|
| 219 |
+
record = f.read_record('<f4', '<i4')
|
| 220 |
+
a = record[0] # first number
|
| 221 |
+
b = record[1] # second number
|
| 222 |
+
|
| 223 |
+
and if any of the variables are arrays, the shape can be specified as
|
| 224 |
+
the third item in the relevant dtype::
|
| 225 |
+
|
| 226 |
+
double precision :: a
|
| 227 |
+
integer :: b(3,4)
|
| 228 |
+
write(1) a, b
|
| 229 |
+
|
| 230 |
+
record = f.read_record('<f4', np.dtype(('<i4', (4, 3))))
|
| 231 |
+
a = record[0]
|
| 232 |
+
b = record[1].T
|
| 233 |
+
|
| 234 |
+
NumPy also supports a short syntax for this kind of type::
|
| 235 |
+
|
| 236 |
+
record = f.read_record('<f4', '(3,3)<i4')
|
| 237 |
+
|
| 238 |
+
See Also
|
| 239 |
+
--------
|
| 240 |
+
read_reals
|
| 241 |
+
read_ints
|
| 242 |
+
|
| 243 |
+
"""
|
| 244 |
+
dtype = kwargs.pop('dtype', None)
|
| 245 |
+
if kwargs:
|
| 246 |
+
raise ValueError(f"Unknown keyword arguments {tuple(kwargs.keys())}")
|
| 247 |
+
|
| 248 |
+
if dtype is not None:
|
| 249 |
+
dtypes = dtypes + (dtype,)
|
| 250 |
+
elif not dtypes:
|
| 251 |
+
raise ValueError('Must specify at least one dtype')
|
| 252 |
+
|
| 253 |
+
first_size = self._read_size(eof_ok=True)
|
| 254 |
+
|
| 255 |
+
dtypes = tuple(np.dtype(dtype) for dtype in dtypes)
|
| 256 |
+
block_size = sum(dtype.itemsize for dtype in dtypes)
|
| 257 |
+
|
| 258 |
+
num_blocks, remainder = divmod(first_size, block_size)
|
| 259 |
+
if remainder != 0:
|
| 260 |
+
raise ValueError(f'Size obtained ({first_size}) is not a multiple of the '
|
| 261 |
+
f'dtypes given ({block_size}).')
|
| 262 |
+
|
| 263 |
+
if len(dtypes) != 1 and first_size != block_size:
|
| 264 |
+
# Fortran does not write mixed type array items in interleaved order,
|
| 265 |
+
# and it's not possible to guess the sizes of the arrays that were written.
|
| 266 |
+
# The user must specify the exact sizes of each of the arrays.
|
| 267 |
+
raise ValueError(f'Size obtained ({first_size}) does not match with the '
|
| 268 |
+
f'expected size ({block_size}) of multi-item record')
|
| 269 |
+
|
| 270 |
+
data = []
|
| 271 |
+
for dtype in dtypes:
|
| 272 |
+
r = np.fromfile(self._fp, dtype=dtype, count=num_blocks)
|
| 273 |
+
if len(r) != num_blocks:
|
| 274 |
+
raise FortranFormattingError(
|
| 275 |
+
"End of file in the middle of a record")
|
| 276 |
+
if dtype.shape != ():
|
| 277 |
+
# Squeeze outmost block dimension for array items
|
| 278 |
+
if num_blocks == 1:
|
| 279 |
+
assert r.shape == (1,) + dtype.shape
|
| 280 |
+
r = r[0]
|
| 281 |
+
|
| 282 |
+
data.append(r)
|
| 283 |
+
|
| 284 |
+
second_size = self._read_size()
|
| 285 |
+
if first_size != second_size:
|
| 286 |
+
raise ValueError('Sizes do not agree in the header and footer for '
|
| 287 |
+
'this record - check header dtype')
|
| 288 |
+
|
| 289 |
+
# Unpack result
|
| 290 |
+
if len(dtypes) == 1:
|
| 291 |
+
return data[0]
|
| 292 |
+
else:
|
| 293 |
+
return tuple(data)
|
| 294 |
+
|
| 295 |
+
def read_ints(self, dtype='i4'):
|
| 296 |
+
"""
|
| 297 |
+
Reads a record of a given type from the file, defaulting to an integer
|
| 298 |
+
type (``INTEGER*4`` in Fortran).
|
| 299 |
+
|
| 300 |
+
Parameters
|
| 301 |
+
----------
|
| 302 |
+
dtype : dtype, optional
|
| 303 |
+
Data type specifying the size and endianness of the data.
|
| 304 |
+
|
| 305 |
+
Returns
|
| 306 |
+
-------
|
| 307 |
+
data : ndarray
|
| 308 |
+
A 1-D array object.
|
| 309 |
+
|
| 310 |
+
See Also
|
| 311 |
+
--------
|
| 312 |
+
read_reals
|
| 313 |
+
read_record
|
| 314 |
+
|
| 315 |
+
"""
|
| 316 |
+
return self.read_record(dtype)
|
| 317 |
+
|
| 318 |
+
def read_reals(self, dtype='f8'):
|
| 319 |
+
"""
|
| 320 |
+
Reads a record of a given type from the file, defaulting to a floating
|
| 321 |
+
point number (``real*8`` in Fortran).
|
| 322 |
+
|
| 323 |
+
Parameters
|
| 324 |
+
----------
|
| 325 |
+
dtype : dtype, optional
|
| 326 |
+
Data type specifying the size and endianness of the data.
|
| 327 |
+
|
| 328 |
+
Returns
|
| 329 |
+
-------
|
| 330 |
+
data : ndarray
|
| 331 |
+
A 1-D array object.
|
| 332 |
+
|
| 333 |
+
See Also
|
| 334 |
+
--------
|
| 335 |
+
read_ints
|
| 336 |
+
read_record
|
| 337 |
+
|
| 338 |
+
"""
|
| 339 |
+
return self.read_record(dtype)
|
| 340 |
+
|
| 341 |
+
def close(self):
|
| 342 |
+
"""
|
| 343 |
+
Closes the file. It is unsupported to call any other methods off this
|
| 344 |
+
object after closing it. Note that this class supports the 'with'
|
| 345 |
+
statement in modern versions of Python, to call this automatically
|
| 346 |
+
|
| 347 |
+
"""
|
| 348 |
+
self._fp.close()
|
| 349 |
+
|
| 350 |
+
def __enter__(self):
|
| 351 |
+
return self
|
| 352 |
+
|
| 353 |
+
def __exit__(self, type, value, tb):
|
| 354 |
+
self.close()
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__init__.py
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from .hb import (MalformedHeader, hb_read, hb_write, HBInfo,
|
| 2 |
+
HBFile, HBMatrixType)
|
| 3 |
+
from ._fortran_format_parser import (FortranFormatParser, IntFormat,
|
| 4 |
+
ExpFormat, BadFortranFormat)
|
| 5 |
+
|
| 6 |
+
# Deprecated namespaces, to be removed in v2.0.0
|
| 7 |
+
from . import hb
|
| 8 |
+
|
| 9 |
+
__all__ = [
|
| 10 |
+
'MalformedHeader', 'hb_read', 'hb_write', 'HBInfo',
|
| 11 |
+
'HBFile', 'HBMatrixType', 'FortranFormatParser', 'IntFormat',
|
| 12 |
+
'ExpFormat', 'BadFortranFormat', 'hb'
|
| 13 |
+
]
|
| 14 |
+
|
| 15 |
+
from scipy._lib._testutils import PytestTester
|
| 16 |
+
test = PytestTester(__name__)
|
| 17 |
+
del PytestTester
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__pycache__/__init__.cpython-310.pyc
ADDED
|
Binary file (641 Bytes). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__pycache__/_fortran_format_parser.cpython-310.pyc
ADDED
|
Binary file (8.9 kB). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/__pycache__/hb.cpython-310.pyc
ADDED
|
Binary file (15.3 kB). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/_fortran_format_parser.py
ADDED
|
@@ -0,0 +1,309 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""
|
| 2 |
+
Preliminary module to handle Fortran formats for IO. Does not use this outside
|
| 3 |
+
scipy.sparse io for now, until the API is deemed reasonable.
|
| 4 |
+
|
| 5 |
+
The *Format classes handle conversion between Fortran and Python format, and
|
| 6 |
+
FortranFormatParser can create *Format instances from raw Fortran format
|
| 7 |
+
strings (e.g. '(3I4)', '(10I3)', etc...)
|
| 8 |
+
"""
|
| 9 |
+
import re
|
| 10 |
+
|
| 11 |
+
import numpy as np
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
__all__ = ["BadFortranFormat", "FortranFormatParser", "IntFormat", "ExpFormat"]
|
| 15 |
+
|
| 16 |
+
|
| 17 |
+
TOKENS = {
|
| 18 |
+
"LPAR": r"\(",
|
| 19 |
+
"RPAR": r"\)",
|
| 20 |
+
"INT_ID": r"I",
|
| 21 |
+
"EXP_ID": r"E",
|
| 22 |
+
"INT": r"\d+",
|
| 23 |
+
"DOT": r"\.",
|
| 24 |
+
}
|
| 25 |
+
|
| 26 |
+
|
| 27 |
+
class BadFortranFormat(SyntaxError):
|
| 28 |
+
pass
|
| 29 |
+
|
| 30 |
+
|
| 31 |
+
def number_digits(n):
|
| 32 |
+
return int(np.floor(np.log10(np.abs(n))) + 1)
|
| 33 |
+
|
| 34 |
+
|
| 35 |
+
class IntFormat:
|
| 36 |
+
@classmethod
|
| 37 |
+
def from_number(cls, n, min=None):
|
| 38 |
+
"""Given an integer, returns a "reasonable" IntFormat instance to represent
|
| 39 |
+
any number between 0 and n if n > 0, -n and n if n < 0
|
| 40 |
+
|
| 41 |
+
Parameters
|
| 42 |
+
----------
|
| 43 |
+
n : int
|
| 44 |
+
max number one wants to be able to represent
|
| 45 |
+
min : int
|
| 46 |
+
minimum number of characters to use for the format
|
| 47 |
+
|
| 48 |
+
Returns
|
| 49 |
+
-------
|
| 50 |
+
res : IntFormat
|
| 51 |
+
IntFormat instance with reasonable (see Notes) computed width
|
| 52 |
+
|
| 53 |
+
Notes
|
| 54 |
+
-----
|
| 55 |
+
Reasonable should be understood as the minimal string length necessary
|
| 56 |
+
without losing precision. For example, IntFormat.from_number(1) will
|
| 57 |
+
return an IntFormat instance of width 2, so that any 0 and 1 may be
|
| 58 |
+
represented as 1-character strings without loss of information.
|
| 59 |
+
"""
|
| 60 |
+
width = number_digits(n) + 1
|
| 61 |
+
if n < 0:
|
| 62 |
+
width += 1
|
| 63 |
+
repeat = 80 // width
|
| 64 |
+
return cls(width, min, repeat=repeat)
|
| 65 |
+
|
| 66 |
+
def __init__(self, width, min=None, repeat=None):
|
| 67 |
+
self.width = width
|
| 68 |
+
self.repeat = repeat
|
| 69 |
+
self.min = min
|
| 70 |
+
|
| 71 |
+
def __repr__(self):
|
| 72 |
+
r = "IntFormat("
|
| 73 |
+
if self.repeat:
|
| 74 |
+
r += "%d" % self.repeat
|
| 75 |
+
r += "I%d" % self.width
|
| 76 |
+
if self.min:
|
| 77 |
+
r += ".%d" % self.min
|
| 78 |
+
return r + ")"
|
| 79 |
+
|
| 80 |
+
@property
|
| 81 |
+
def fortran_format(self):
|
| 82 |
+
r = "("
|
| 83 |
+
if self.repeat:
|
| 84 |
+
r += "%d" % self.repeat
|
| 85 |
+
r += "I%d" % self.width
|
| 86 |
+
if self.min:
|
| 87 |
+
r += ".%d" % self.min
|
| 88 |
+
return r + ")"
|
| 89 |
+
|
| 90 |
+
@property
|
| 91 |
+
def python_format(self):
|
| 92 |
+
return "%" + str(self.width) + "d"
|
| 93 |
+
|
| 94 |
+
|
| 95 |
+
class ExpFormat:
|
| 96 |
+
@classmethod
|
| 97 |
+
def from_number(cls, n, min=None):
|
| 98 |
+
"""Given a float number, returns a "reasonable" ExpFormat instance to
|
| 99 |
+
represent any number between -n and n.
|
| 100 |
+
|
| 101 |
+
Parameters
|
| 102 |
+
----------
|
| 103 |
+
n : float
|
| 104 |
+
max number one wants to be able to represent
|
| 105 |
+
min : int
|
| 106 |
+
minimum number of characters to use for the format
|
| 107 |
+
|
| 108 |
+
Returns
|
| 109 |
+
-------
|
| 110 |
+
res : ExpFormat
|
| 111 |
+
ExpFormat instance with reasonable (see Notes) computed width
|
| 112 |
+
|
| 113 |
+
Notes
|
| 114 |
+
-----
|
| 115 |
+
Reasonable should be understood as the minimal string length necessary
|
| 116 |
+
to avoid losing precision.
|
| 117 |
+
"""
|
| 118 |
+
# len of one number in exp format: sign + 1|0 + "." +
|
| 119 |
+
# number of digit for fractional part + 'E' + sign of exponent +
|
| 120 |
+
# len of exponent
|
| 121 |
+
finfo = np.finfo(n.dtype)
|
| 122 |
+
# Number of digits for fractional part
|
| 123 |
+
n_prec = finfo.precision + 1
|
| 124 |
+
# Number of digits for exponential part
|
| 125 |
+
n_exp = number_digits(np.max(np.abs([finfo.maxexp, finfo.minexp])))
|
| 126 |
+
width = 1 + 1 + n_prec + 1 + n_exp + 1
|
| 127 |
+
if n < 0:
|
| 128 |
+
width += 1
|
| 129 |
+
repeat = int(np.floor(80 / width))
|
| 130 |
+
return cls(width, n_prec, min, repeat=repeat)
|
| 131 |
+
|
| 132 |
+
def __init__(self, width, significand, min=None, repeat=None):
|
| 133 |
+
"""\
|
| 134 |
+
Parameters
|
| 135 |
+
----------
|
| 136 |
+
width : int
|
| 137 |
+
number of characters taken by the string (includes space).
|
| 138 |
+
"""
|
| 139 |
+
self.width = width
|
| 140 |
+
self.significand = significand
|
| 141 |
+
self.repeat = repeat
|
| 142 |
+
self.min = min
|
| 143 |
+
|
| 144 |
+
def __repr__(self):
|
| 145 |
+
r = "ExpFormat("
|
| 146 |
+
if self.repeat:
|
| 147 |
+
r += "%d" % self.repeat
|
| 148 |
+
r += "E%d.%d" % (self.width, self.significand)
|
| 149 |
+
if self.min:
|
| 150 |
+
r += "E%d" % self.min
|
| 151 |
+
return r + ")"
|
| 152 |
+
|
| 153 |
+
@property
|
| 154 |
+
def fortran_format(self):
|
| 155 |
+
r = "("
|
| 156 |
+
if self.repeat:
|
| 157 |
+
r += "%d" % self.repeat
|
| 158 |
+
r += "E%d.%d" % (self.width, self.significand)
|
| 159 |
+
if self.min:
|
| 160 |
+
r += "E%d" % self.min
|
| 161 |
+
return r + ")"
|
| 162 |
+
|
| 163 |
+
@property
|
| 164 |
+
def python_format(self):
|
| 165 |
+
return "%" + str(self.width-1) + "." + str(self.significand) + "E"
|
| 166 |
+
|
| 167 |
+
|
| 168 |
+
class Token:
|
| 169 |
+
def __init__(self, type, value, pos):
|
| 170 |
+
self.type = type
|
| 171 |
+
self.value = value
|
| 172 |
+
self.pos = pos
|
| 173 |
+
|
| 174 |
+
def __str__(self):
|
| 175 |
+
return f"""Token('{self.type}', "{self.value}")"""
|
| 176 |
+
|
| 177 |
+
def __repr__(self):
|
| 178 |
+
return self.__str__()
|
| 179 |
+
|
| 180 |
+
|
| 181 |
+
class Tokenizer:
|
| 182 |
+
def __init__(self):
|
| 183 |
+
self.tokens = list(TOKENS.keys())
|
| 184 |
+
self.res = [re.compile(TOKENS[i]) for i in self.tokens]
|
| 185 |
+
|
| 186 |
+
def input(self, s):
|
| 187 |
+
self.data = s
|
| 188 |
+
self.curpos = 0
|
| 189 |
+
self.len = len(s)
|
| 190 |
+
|
| 191 |
+
def next_token(self):
|
| 192 |
+
curpos = self.curpos
|
| 193 |
+
|
| 194 |
+
while curpos < self.len:
|
| 195 |
+
for i, r in enumerate(self.res):
|
| 196 |
+
m = r.match(self.data, curpos)
|
| 197 |
+
if m is None:
|
| 198 |
+
continue
|
| 199 |
+
else:
|
| 200 |
+
self.curpos = m.end()
|
| 201 |
+
return Token(self.tokens[i], m.group(), self.curpos)
|
| 202 |
+
raise SyntaxError("Unknown character at position %d (%s)"
|
| 203 |
+
% (self.curpos, self.data[curpos]))
|
| 204 |
+
|
| 205 |
+
|
| 206 |
+
# Grammar for fortran format:
|
| 207 |
+
# format : LPAR format_string RPAR
|
| 208 |
+
# format_string : repeated | simple
|
| 209 |
+
# repeated : repeat simple
|
| 210 |
+
# simple : int_fmt | exp_fmt
|
| 211 |
+
# int_fmt : INT_ID width
|
| 212 |
+
# exp_fmt : simple_exp_fmt
|
| 213 |
+
# simple_exp_fmt : EXP_ID width DOT significand
|
| 214 |
+
# extended_exp_fmt : EXP_ID width DOT significand EXP_ID ndigits
|
| 215 |
+
# repeat : INT
|
| 216 |
+
# width : INT
|
| 217 |
+
# significand : INT
|
| 218 |
+
# ndigits : INT
|
| 219 |
+
|
| 220 |
+
# Naive fortran formatter - parser is hand-made
|
| 221 |
+
class FortranFormatParser:
|
| 222 |
+
"""Parser for Fortran format strings. The parse method returns a *Format
|
| 223 |
+
instance.
|
| 224 |
+
|
| 225 |
+
Notes
|
| 226 |
+
-----
|
| 227 |
+
Only ExpFormat (exponential format for floating values) and IntFormat
|
| 228 |
+
(integer format) for now.
|
| 229 |
+
"""
|
| 230 |
+
def __init__(self):
|
| 231 |
+
self.tokenizer = Tokenizer()
|
| 232 |
+
|
| 233 |
+
def parse(self, s):
|
| 234 |
+
self.tokenizer.input(s)
|
| 235 |
+
|
| 236 |
+
tokens = []
|
| 237 |
+
|
| 238 |
+
try:
|
| 239 |
+
while True:
|
| 240 |
+
t = self.tokenizer.next_token()
|
| 241 |
+
if t is None:
|
| 242 |
+
break
|
| 243 |
+
else:
|
| 244 |
+
tokens.append(t)
|
| 245 |
+
return self._parse_format(tokens)
|
| 246 |
+
except SyntaxError as e:
|
| 247 |
+
raise BadFortranFormat(str(e)) from e
|
| 248 |
+
|
| 249 |
+
def _get_min(self, tokens):
|
| 250 |
+
next = tokens.pop(0)
|
| 251 |
+
if not next.type == "DOT":
|
| 252 |
+
raise SyntaxError()
|
| 253 |
+
next = tokens.pop(0)
|
| 254 |
+
return next.value
|
| 255 |
+
|
| 256 |
+
def _expect(self, token, tp):
|
| 257 |
+
if not token.type == tp:
|
| 258 |
+
raise SyntaxError()
|
| 259 |
+
|
| 260 |
+
def _parse_format(self, tokens):
|
| 261 |
+
if not tokens[0].type == "LPAR":
|
| 262 |
+
raise SyntaxError("Expected left parenthesis at position "
|
| 263 |
+
"%d (got '%s')" % (0, tokens[0].value))
|
| 264 |
+
elif not tokens[-1].type == "RPAR":
|
| 265 |
+
raise SyntaxError("Expected right parenthesis at position "
|
| 266 |
+
"%d (got '%s')" % (len(tokens), tokens[-1].value))
|
| 267 |
+
|
| 268 |
+
tokens = tokens[1:-1]
|
| 269 |
+
types = [t.type for t in tokens]
|
| 270 |
+
if types[0] == "INT":
|
| 271 |
+
repeat = int(tokens.pop(0).value)
|
| 272 |
+
else:
|
| 273 |
+
repeat = None
|
| 274 |
+
|
| 275 |
+
next = tokens.pop(0)
|
| 276 |
+
if next.type == "INT_ID":
|
| 277 |
+
next = self._next(tokens, "INT")
|
| 278 |
+
width = int(next.value)
|
| 279 |
+
if tokens:
|
| 280 |
+
min = int(self._get_min(tokens))
|
| 281 |
+
else:
|
| 282 |
+
min = None
|
| 283 |
+
return IntFormat(width, min, repeat)
|
| 284 |
+
elif next.type == "EXP_ID":
|
| 285 |
+
next = self._next(tokens, "INT")
|
| 286 |
+
width = int(next.value)
|
| 287 |
+
|
| 288 |
+
next = self._next(tokens, "DOT")
|
| 289 |
+
|
| 290 |
+
next = self._next(tokens, "INT")
|
| 291 |
+
significand = int(next.value)
|
| 292 |
+
|
| 293 |
+
if tokens:
|
| 294 |
+
next = self._next(tokens, "EXP_ID")
|
| 295 |
+
|
| 296 |
+
next = self._next(tokens, "INT")
|
| 297 |
+
min = int(next.value)
|
| 298 |
+
else:
|
| 299 |
+
min = None
|
| 300 |
+
return ExpFormat(width, significand, min, repeat)
|
| 301 |
+
else:
|
| 302 |
+
raise SyntaxError("Invalid formatter type %s" % next.value)
|
| 303 |
+
|
| 304 |
+
def _next(self, tokens, tp):
|
| 305 |
+
if not len(tokens) > 0:
|
| 306 |
+
raise SyntaxError()
|
| 307 |
+
next = tokens.pop(0)
|
| 308 |
+
self._expect(next, tp)
|
| 309 |
+
return next
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/hb.py
ADDED
|
@@ -0,0 +1,571 @@
|
|
|
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|
|
|
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|
|
|
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
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|
|
|
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|
|
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|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
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|
|
|
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|
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|
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|
|
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|
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|
|
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|
|
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|
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|
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|
|
|
|
| 1 |
+
"""
|
| 2 |
+
Implementation of Harwell-Boeing read/write.
|
| 3 |
+
|
| 4 |
+
At the moment not the full Harwell-Boeing format is supported. Supported
|
| 5 |
+
features are:
|
| 6 |
+
|
| 7 |
+
- assembled, non-symmetric, real matrices
|
| 8 |
+
- integer for pointer/indices
|
| 9 |
+
- exponential format for float values, and int format
|
| 10 |
+
|
| 11 |
+
"""
|
| 12 |
+
# TODO:
|
| 13 |
+
# - Add more support (symmetric/complex matrices, non-assembled matrices ?)
|
| 14 |
+
|
| 15 |
+
# XXX: reading is reasonably efficient (>= 85 % is in numpy.fromstring), but
|
| 16 |
+
# takes a lot of memory. Being faster would require compiled code.
|
| 17 |
+
# write is not efficient. Although not a terribly exciting task,
|
| 18 |
+
# having reusable facilities to efficiently read/write fortran-formatted files
|
| 19 |
+
# would be useful outside this module.
|
| 20 |
+
|
| 21 |
+
import warnings
|
| 22 |
+
|
| 23 |
+
import numpy as np
|
| 24 |
+
from scipy.sparse import csc_matrix
|
| 25 |
+
from ._fortran_format_parser import FortranFormatParser, IntFormat, ExpFormat
|
| 26 |
+
|
| 27 |
+
__all__ = ["MalformedHeader", "hb_read", "hb_write", "HBInfo", "HBFile",
|
| 28 |
+
"HBMatrixType"]
|
| 29 |
+
|
| 30 |
+
|
| 31 |
+
class MalformedHeader(Exception):
|
| 32 |
+
pass
|
| 33 |
+
|
| 34 |
+
|
| 35 |
+
class LineOverflow(Warning):
|
| 36 |
+
pass
|
| 37 |
+
|
| 38 |
+
|
| 39 |
+
def _nbytes_full(fmt, nlines):
|
| 40 |
+
"""Return the number of bytes to read to get every full lines for the
|
| 41 |
+
given parsed fortran format."""
|
| 42 |
+
return (fmt.repeat * fmt.width + 1) * (nlines - 1)
|
| 43 |
+
|
| 44 |
+
|
| 45 |
+
class HBInfo:
|
| 46 |
+
@classmethod
|
| 47 |
+
def from_data(cls, m, title="Default title", key="0", mxtype=None, fmt=None):
|
| 48 |
+
"""Create a HBInfo instance from an existing sparse matrix.
|
| 49 |
+
|
| 50 |
+
Parameters
|
| 51 |
+
----------
|
| 52 |
+
m : sparse matrix
|
| 53 |
+
the HBInfo instance will derive its parameters from m
|
| 54 |
+
title : str
|
| 55 |
+
Title to put in the HB header
|
| 56 |
+
key : str
|
| 57 |
+
Key
|
| 58 |
+
mxtype : HBMatrixType
|
| 59 |
+
type of the input matrix
|
| 60 |
+
fmt : dict
|
| 61 |
+
not implemented
|
| 62 |
+
|
| 63 |
+
Returns
|
| 64 |
+
-------
|
| 65 |
+
hb_info : HBInfo instance
|
| 66 |
+
"""
|
| 67 |
+
m = m.tocsc(copy=False)
|
| 68 |
+
|
| 69 |
+
pointer = m.indptr
|
| 70 |
+
indices = m.indices
|
| 71 |
+
values = m.data
|
| 72 |
+
|
| 73 |
+
nrows, ncols = m.shape
|
| 74 |
+
nnon_zeros = m.nnz
|
| 75 |
+
|
| 76 |
+
if fmt is None:
|
| 77 |
+
# +1 because HB use one-based indexing (Fortran), and we will write
|
| 78 |
+
# the indices /pointer as such
|
| 79 |
+
pointer_fmt = IntFormat.from_number(np.max(pointer+1))
|
| 80 |
+
indices_fmt = IntFormat.from_number(np.max(indices+1))
|
| 81 |
+
|
| 82 |
+
if values.dtype.kind in np.typecodes["AllFloat"]:
|
| 83 |
+
values_fmt = ExpFormat.from_number(-np.max(np.abs(values)))
|
| 84 |
+
elif values.dtype.kind in np.typecodes["AllInteger"]:
|
| 85 |
+
values_fmt = IntFormat.from_number(-np.max(np.abs(values)))
|
| 86 |
+
else:
|
| 87 |
+
message = f"type {values.dtype.kind} not implemented yet"
|
| 88 |
+
raise NotImplementedError(message)
|
| 89 |
+
else:
|
| 90 |
+
raise NotImplementedError("fmt argument not supported yet.")
|
| 91 |
+
|
| 92 |
+
if mxtype is None:
|
| 93 |
+
if not np.isrealobj(values):
|
| 94 |
+
raise ValueError("Complex values not supported yet")
|
| 95 |
+
if values.dtype.kind in np.typecodes["AllInteger"]:
|
| 96 |
+
tp = "integer"
|
| 97 |
+
elif values.dtype.kind in np.typecodes["AllFloat"]:
|
| 98 |
+
tp = "real"
|
| 99 |
+
else:
|
| 100 |
+
raise NotImplementedError("type %s for values not implemented"
|
| 101 |
+
% values.dtype)
|
| 102 |
+
mxtype = HBMatrixType(tp, "unsymmetric", "assembled")
|
| 103 |
+
else:
|
| 104 |
+
raise ValueError("mxtype argument not handled yet.")
|
| 105 |
+
|
| 106 |
+
def _nlines(fmt, size):
|
| 107 |
+
nlines = size // fmt.repeat
|
| 108 |
+
if nlines * fmt.repeat != size:
|
| 109 |
+
nlines += 1
|
| 110 |
+
return nlines
|
| 111 |
+
|
| 112 |
+
pointer_nlines = _nlines(pointer_fmt, pointer.size)
|
| 113 |
+
indices_nlines = _nlines(indices_fmt, indices.size)
|
| 114 |
+
values_nlines = _nlines(values_fmt, values.size)
|
| 115 |
+
|
| 116 |
+
total_nlines = pointer_nlines + indices_nlines + values_nlines
|
| 117 |
+
|
| 118 |
+
return cls(title, key,
|
| 119 |
+
total_nlines, pointer_nlines, indices_nlines, values_nlines,
|
| 120 |
+
mxtype, nrows, ncols, nnon_zeros,
|
| 121 |
+
pointer_fmt.fortran_format, indices_fmt.fortran_format,
|
| 122 |
+
values_fmt.fortran_format)
|
| 123 |
+
|
| 124 |
+
@classmethod
|
| 125 |
+
def from_file(cls, fid):
|
| 126 |
+
"""Create a HBInfo instance from a file object containing a matrix in the
|
| 127 |
+
HB format.
|
| 128 |
+
|
| 129 |
+
Parameters
|
| 130 |
+
----------
|
| 131 |
+
fid : file-like matrix
|
| 132 |
+
File or file-like object containing a matrix in the HB format.
|
| 133 |
+
|
| 134 |
+
Returns
|
| 135 |
+
-------
|
| 136 |
+
hb_info : HBInfo instance
|
| 137 |
+
"""
|
| 138 |
+
# First line
|
| 139 |
+
line = fid.readline().strip("\n")
|
| 140 |
+
if not len(line) > 72:
|
| 141 |
+
raise ValueError("Expected at least 72 characters for first line, "
|
| 142 |
+
"got: \n%s" % line)
|
| 143 |
+
title = line[:72]
|
| 144 |
+
key = line[72:]
|
| 145 |
+
|
| 146 |
+
# Second line
|
| 147 |
+
line = fid.readline().strip("\n")
|
| 148 |
+
if not len(line.rstrip()) >= 56:
|
| 149 |
+
raise ValueError("Expected at least 56 characters for second line, "
|
| 150 |
+
"got: \n%s" % line)
|
| 151 |
+
total_nlines = _expect_int(line[:14])
|
| 152 |
+
pointer_nlines = _expect_int(line[14:28])
|
| 153 |
+
indices_nlines = _expect_int(line[28:42])
|
| 154 |
+
values_nlines = _expect_int(line[42:56])
|
| 155 |
+
|
| 156 |
+
rhs_nlines = line[56:72].strip()
|
| 157 |
+
if rhs_nlines == '':
|
| 158 |
+
rhs_nlines = 0
|
| 159 |
+
else:
|
| 160 |
+
rhs_nlines = _expect_int(rhs_nlines)
|
| 161 |
+
if not rhs_nlines == 0:
|
| 162 |
+
raise ValueError("Only files without right hand side supported for "
|
| 163 |
+
"now.")
|
| 164 |
+
|
| 165 |
+
# Third line
|
| 166 |
+
line = fid.readline().strip("\n")
|
| 167 |
+
if not len(line) >= 70:
|
| 168 |
+
raise ValueError("Expected at least 72 character for third line, got:\n"
|
| 169 |
+
"%s" % line)
|
| 170 |
+
|
| 171 |
+
mxtype_s = line[:3].upper()
|
| 172 |
+
if not len(mxtype_s) == 3:
|
| 173 |
+
raise ValueError("mxtype expected to be 3 characters long")
|
| 174 |
+
|
| 175 |
+
mxtype = HBMatrixType.from_fortran(mxtype_s)
|
| 176 |
+
if mxtype.value_type not in ["real", "integer"]:
|
| 177 |
+
raise ValueError("Only real or integer matrices supported for "
|
| 178 |
+
"now (detected %s)" % mxtype)
|
| 179 |
+
if not mxtype.structure == "unsymmetric":
|
| 180 |
+
raise ValueError("Only unsymmetric matrices supported for "
|
| 181 |
+
"now (detected %s)" % mxtype)
|
| 182 |
+
if not mxtype.storage == "assembled":
|
| 183 |
+
raise ValueError("Only assembled matrices supported for now")
|
| 184 |
+
|
| 185 |
+
if not line[3:14] == " " * 11:
|
| 186 |
+
raise ValueError("Malformed data for third line: %s" % line)
|
| 187 |
+
|
| 188 |
+
nrows = _expect_int(line[14:28])
|
| 189 |
+
ncols = _expect_int(line[28:42])
|
| 190 |
+
nnon_zeros = _expect_int(line[42:56])
|
| 191 |
+
nelementals = _expect_int(line[56:70])
|
| 192 |
+
if not nelementals == 0:
|
| 193 |
+
raise ValueError("Unexpected value %d for nltvl (last entry of line 3)"
|
| 194 |
+
% nelementals)
|
| 195 |
+
|
| 196 |
+
# Fourth line
|
| 197 |
+
line = fid.readline().strip("\n")
|
| 198 |
+
|
| 199 |
+
ct = line.split()
|
| 200 |
+
if not len(ct) == 3:
|
| 201 |
+
raise ValueError("Expected 3 formats, got %s" % ct)
|
| 202 |
+
|
| 203 |
+
return cls(title, key,
|
| 204 |
+
total_nlines, pointer_nlines, indices_nlines, values_nlines,
|
| 205 |
+
mxtype, nrows, ncols, nnon_zeros,
|
| 206 |
+
ct[0], ct[1], ct[2],
|
| 207 |
+
rhs_nlines, nelementals)
|
| 208 |
+
|
| 209 |
+
def __init__(self, title, key,
|
| 210 |
+
total_nlines, pointer_nlines, indices_nlines, values_nlines,
|
| 211 |
+
mxtype, nrows, ncols, nnon_zeros,
|
| 212 |
+
pointer_format_str, indices_format_str, values_format_str,
|
| 213 |
+
right_hand_sides_nlines=0, nelementals=0):
|
| 214 |
+
"""Do not use this directly, but the class ctrs (from_* functions)."""
|
| 215 |
+
self.title = title
|
| 216 |
+
self.key = key
|
| 217 |
+
if title is None:
|
| 218 |
+
title = "No Title"
|
| 219 |
+
if len(title) > 72:
|
| 220 |
+
raise ValueError("title cannot be > 72 characters")
|
| 221 |
+
|
| 222 |
+
if key is None:
|
| 223 |
+
key = "|No Key"
|
| 224 |
+
if len(key) > 8:
|
| 225 |
+
warnings.warn("key is > 8 characters (key is %s)" % key,
|
| 226 |
+
LineOverflow, stacklevel=3)
|
| 227 |
+
|
| 228 |
+
self.total_nlines = total_nlines
|
| 229 |
+
self.pointer_nlines = pointer_nlines
|
| 230 |
+
self.indices_nlines = indices_nlines
|
| 231 |
+
self.values_nlines = values_nlines
|
| 232 |
+
|
| 233 |
+
parser = FortranFormatParser()
|
| 234 |
+
pointer_format = parser.parse(pointer_format_str)
|
| 235 |
+
if not isinstance(pointer_format, IntFormat):
|
| 236 |
+
raise ValueError("Expected int format for pointer format, got %s"
|
| 237 |
+
% pointer_format)
|
| 238 |
+
|
| 239 |
+
indices_format = parser.parse(indices_format_str)
|
| 240 |
+
if not isinstance(indices_format, IntFormat):
|
| 241 |
+
raise ValueError("Expected int format for indices format, got %s" %
|
| 242 |
+
indices_format)
|
| 243 |
+
|
| 244 |
+
values_format = parser.parse(values_format_str)
|
| 245 |
+
if isinstance(values_format, ExpFormat):
|
| 246 |
+
if mxtype.value_type not in ["real", "complex"]:
|
| 247 |
+
raise ValueError(f"Inconsistency between matrix type {mxtype} and "
|
| 248 |
+
f"value type {values_format}")
|
| 249 |
+
values_dtype = np.float64
|
| 250 |
+
elif isinstance(values_format, IntFormat):
|
| 251 |
+
if mxtype.value_type not in ["integer"]:
|
| 252 |
+
raise ValueError(f"Inconsistency between matrix type {mxtype} and "
|
| 253 |
+
f"value type {values_format}")
|
| 254 |
+
# XXX: fortran int -> dtype association ?
|
| 255 |
+
values_dtype = int
|
| 256 |
+
else:
|
| 257 |
+
raise ValueError(f"Unsupported format for values {values_format!r}")
|
| 258 |
+
|
| 259 |
+
self.pointer_format = pointer_format
|
| 260 |
+
self.indices_format = indices_format
|
| 261 |
+
self.values_format = values_format
|
| 262 |
+
|
| 263 |
+
self.pointer_dtype = np.int32
|
| 264 |
+
self.indices_dtype = np.int32
|
| 265 |
+
self.values_dtype = values_dtype
|
| 266 |
+
|
| 267 |
+
self.pointer_nlines = pointer_nlines
|
| 268 |
+
self.pointer_nbytes_full = _nbytes_full(pointer_format, pointer_nlines)
|
| 269 |
+
|
| 270 |
+
self.indices_nlines = indices_nlines
|
| 271 |
+
self.indices_nbytes_full = _nbytes_full(indices_format, indices_nlines)
|
| 272 |
+
|
| 273 |
+
self.values_nlines = values_nlines
|
| 274 |
+
self.values_nbytes_full = _nbytes_full(values_format, values_nlines)
|
| 275 |
+
|
| 276 |
+
self.nrows = nrows
|
| 277 |
+
self.ncols = ncols
|
| 278 |
+
self.nnon_zeros = nnon_zeros
|
| 279 |
+
self.nelementals = nelementals
|
| 280 |
+
self.mxtype = mxtype
|
| 281 |
+
|
| 282 |
+
def dump(self):
|
| 283 |
+
"""Gives the header corresponding to this instance as a string."""
|
| 284 |
+
header = [self.title.ljust(72) + self.key.ljust(8)]
|
| 285 |
+
|
| 286 |
+
header.append("%14d%14d%14d%14d" %
|
| 287 |
+
(self.total_nlines, self.pointer_nlines,
|
| 288 |
+
self.indices_nlines, self.values_nlines))
|
| 289 |
+
header.append("%14s%14d%14d%14d%14d" %
|
| 290 |
+
(self.mxtype.fortran_format.ljust(14), self.nrows,
|
| 291 |
+
self.ncols, self.nnon_zeros, 0))
|
| 292 |
+
|
| 293 |
+
pffmt = self.pointer_format.fortran_format
|
| 294 |
+
iffmt = self.indices_format.fortran_format
|
| 295 |
+
vffmt = self.values_format.fortran_format
|
| 296 |
+
header.append("%16s%16s%20s" %
|
| 297 |
+
(pffmt.ljust(16), iffmt.ljust(16), vffmt.ljust(20)))
|
| 298 |
+
return "\n".join(header)
|
| 299 |
+
|
| 300 |
+
|
| 301 |
+
def _expect_int(value, msg=None):
|
| 302 |
+
try:
|
| 303 |
+
return int(value)
|
| 304 |
+
except ValueError as e:
|
| 305 |
+
if msg is None:
|
| 306 |
+
msg = "Expected an int, got %s"
|
| 307 |
+
raise ValueError(msg % value) from e
|
| 308 |
+
|
| 309 |
+
|
| 310 |
+
def _read_hb_data(content, header):
|
| 311 |
+
# XXX: look at a way to reduce memory here (big string creation)
|
| 312 |
+
ptr_string = "".join([content.read(header.pointer_nbytes_full),
|
| 313 |
+
content.readline()])
|
| 314 |
+
ptr = np.fromstring(ptr_string,
|
| 315 |
+
dtype=int, sep=' ')
|
| 316 |
+
|
| 317 |
+
ind_string = "".join([content.read(header.indices_nbytes_full),
|
| 318 |
+
content.readline()])
|
| 319 |
+
ind = np.fromstring(ind_string,
|
| 320 |
+
dtype=int, sep=' ')
|
| 321 |
+
|
| 322 |
+
val_string = "".join([content.read(header.values_nbytes_full),
|
| 323 |
+
content.readline()])
|
| 324 |
+
val = np.fromstring(val_string,
|
| 325 |
+
dtype=header.values_dtype, sep=' ')
|
| 326 |
+
|
| 327 |
+
try:
|
| 328 |
+
return csc_matrix((val, ind-1, ptr-1),
|
| 329 |
+
shape=(header.nrows, header.ncols))
|
| 330 |
+
except ValueError as e:
|
| 331 |
+
raise e
|
| 332 |
+
|
| 333 |
+
|
| 334 |
+
def _write_data(m, fid, header):
|
| 335 |
+
m = m.tocsc(copy=False)
|
| 336 |
+
|
| 337 |
+
def write_array(f, ar, nlines, fmt):
|
| 338 |
+
# ar_nlines is the number of full lines, n is the number of items per
|
| 339 |
+
# line, ffmt the fortran format
|
| 340 |
+
pyfmt = fmt.python_format
|
| 341 |
+
pyfmt_full = pyfmt * fmt.repeat
|
| 342 |
+
|
| 343 |
+
# for each array to write, we first write the full lines, and special
|
| 344 |
+
# case for partial line
|
| 345 |
+
full = ar[:(nlines - 1) * fmt.repeat]
|
| 346 |
+
for row in full.reshape((nlines-1, fmt.repeat)):
|
| 347 |
+
f.write(pyfmt_full % tuple(row) + "\n")
|
| 348 |
+
nremain = ar.size - full.size
|
| 349 |
+
if nremain > 0:
|
| 350 |
+
f.write((pyfmt * nremain) % tuple(ar[ar.size - nremain:]) + "\n")
|
| 351 |
+
|
| 352 |
+
fid.write(header.dump())
|
| 353 |
+
fid.write("\n")
|
| 354 |
+
# +1 is for Fortran one-based indexing
|
| 355 |
+
write_array(fid, m.indptr+1, header.pointer_nlines,
|
| 356 |
+
header.pointer_format)
|
| 357 |
+
write_array(fid, m.indices+1, header.indices_nlines,
|
| 358 |
+
header.indices_format)
|
| 359 |
+
write_array(fid, m.data, header.values_nlines,
|
| 360 |
+
header.values_format)
|
| 361 |
+
|
| 362 |
+
|
| 363 |
+
class HBMatrixType:
|
| 364 |
+
"""Class to hold the matrix type."""
|
| 365 |
+
# q2f* translates qualified names to Fortran character
|
| 366 |
+
_q2f_type = {
|
| 367 |
+
"real": "R",
|
| 368 |
+
"complex": "C",
|
| 369 |
+
"pattern": "P",
|
| 370 |
+
"integer": "I",
|
| 371 |
+
}
|
| 372 |
+
_q2f_structure = {
|
| 373 |
+
"symmetric": "S",
|
| 374 |
+
"unsymmetric": "U",
|
| 375 |
+
"hermitian": "H",
|
| 376 |
+
"skewsymmetric": "Z",
|
| 377 |
+
"rectangular": "R"
|
| 378 |
+
}
|
| 379 |
+
_q2f_storage = {
|
| 380 |
+
"assembled": "A",
|
| 381 |
+
"elemental": "E",
|
| 382 |
+
}
|
| 383 |
+
|
| 384 |
+
_f2q_type = {j: i for i, j in _q2f_type.items()}
|
| 385 |
+
_f2q_structure = {j: i for i, j in _q2f_structure.items()}
|
| 386 |
+
_f2q_storage = {j: i for i, j in _q2f_storage.items()}
|
| 387 |
+
|
| 388 |
+
@classmethod
|
| 389 |
+
def from_fortran(cls, fmt):
|
| 390 |
+
if not len(fmt) == 3:
|
| 391 |
+
raise ValueError("Fortran format for matrix type should be 3 "
|
| 392 |
+
"characters long")
|
| 393 |
+
try:
|
| 394 |
+
value_type = cls._f2q_type[fmt[0]]
|
| 395 |
+
structure = cls._f2q_structure[fmt[1]]
|
| 396 |
+
storage = cls._f2q_storage[fmt[2]]
|
| 397 |
+
return cls(value_type, structure, storage)
|
| 398 |
+
except KeyError as e:
|
| 399 |
+
raise ValueError("Unrecognized format %s" % fmt) from e
|
| 400 |
+
|
| 401 |
+
def __init__(self, value_type, structure, storage="assembled"):
|
| 402 |
+
self.value_type = value_type
|
| 403 |
+
self.structure = structure
|
| 404 |
+
self.storage = storage
|
| 405 |
+
|
| 406 |
+
if value_type not in self._q2f_type:
|
| 407 |
+
raise ValueError("Unrecognized type %s" % value_type)
|
| 408 |
+
if structure not in self._q2f_structure:
|
| 409 |
+
raise ValueError("Unrecognized structure %s" % structure)
|
| 410 |
+
if storage not in self._q2f_storage:
|
| 411 |
+
raise ValueError("Unrecognized storage %s" % storage)
|
| 412 |
+
|
| 413 |
+
@property
|
| 414 |
+
def fortran_format(self):
|
| 415 |
+
return self._q2f_type[self.value_type] + \
|
| 416 |
+
self._q2f_structure[self.structure] + \
|
| 417 |
+
self._q2f_storage[self.storage]
|
| 418 |
+
|
| 419 |
+
def __repr__(self):
|
| 420 |
+
return f"HBMatrixType({self.value_type}, {self.structure}, {self.storage})"
|
| 421 |
+
|
| 422 |
+
|
| 423 |
+
class HBFile:
|
| 424 |
+
def __init__(self, file, hb_info=None):
|
| 425 |
+
"""Create a HBFile instance.
|
| 426 |
+
|
| 427 |
+
Parameters
|
| 428 |
+
----------
|
| 429 |
+
file : file-object
|
| 430 |
+
StringIO work as well
|
| 431 |
+
hb_info : HBInfo, optional
|
| 432 |
+
Should be given as an argument for writing, in which case the file
|
| 433 |
+
should be writable.
|
| 434 |
+
"""
|
| 435 |
+
self._fid = file
|
| 436 |
+
if hb_info is None:
|
| 437 |
+
self._hb_info = HBInfo.from_file(file)
|
| 438 |
+
else:
|
| 439 |
+
#raise OSError("file %s is not writable, and hb_info "
|
| 440 |
+
# "was given." % file)
|
| 441 |
+
self._hb_info = hb_info
|
| 442 |
+
|
| 443 |
+
@property
|
| 444 |
+
def title(self):
|
| 445 |
+
return self._hb_info.title
|
| 446 |
+
|
| 447 |
+
@property
|
| 448 |
+
def key(self):
|
| 449 |
+
return self._hb_info.key
|
| 450 |
+
|
| 451 |
+
@property
|
| 452 |
+
def type(self):
|
| 453 |
+
return self._hb_info.mxtype.value_type
|
| 454 |
+
|
| 455 |
+
@property
|
| 456 |
+
def structure(self):
|
| 457 |
+
return self._hb_info.mxtype.structure
|
| 458 |
+
|
| 459 |
+
@property
|
| 460 |
+
def storage(self):
|
| 461 |
+
return self._hb_info.mxtype.storage
|
| 462 |
+
|
| 463 |
+
def read_matrix(self):
|
| 464 |
+
return _read_hb_data(self._fid, self._hb_info)
|
| 465 |
+
|
| 466 |
+
def write_matrix(self, m):
|
| 467 |
+
return _write_data(m, self._fid, self._hb_info)
|
| 468 |
+
|
| 469 |
+
|
| 470 |
+
def hb_read(path_or_open_file):
|
| 471 |
+
"""Read HB-format file.
|
| 472 |
+
|
| 473 |
+
Parameters
|
| 474 |
+
----------
|
| 475 |
+
path_or_open_file : path-like or file-like
|
| 476 |
+
If a file-like object, it is used as-is. Otherwise, it is opened
|
| 477 |
+
before reading.
|
| 478 |
+
|
| 479 |
+
Returns
|
| 480 |
+
-------
|
| 481 |
+
data : scipy.sparse.csc_matrix instance
|
| 482 |
+
The data read from the HB file as a sparse matrix.
|
| 483 |
+
|
| 484 |
+
Notes
|
| 485 |
+
-----
|
| 486 |
+
At the moment not the full Harwell-Boeing format is supported. Supported
|
| 487 |
+
features are:
|
| 488 |
+
|
| 489 |
+
- assembled, non-symmetric, real matrices
|
| 490 |
+
- integer for pointer/indices
|
| 491 |
+
- exponential format for float values, and int format
|
| 492 |
+
|
| 493 |
+
Examples
|
| 494 |
+
--------
|
| 495 |
+
We can read and write a harwell-boeing format file:
|
| 496 |
+
|
| 497 |
+
>>> from scipy.io import hb_read, hb_write
|
| 498 |
+
>>> from scipy.sparse import csr_matrix, eye
|
| 499 |
+
>>> data = csr_matrix(eye(3)) # create a sparse matrix
|
| 500 |
+
>>> hb_write("data.hb", data) # write a hb file
|
| 501 |
+
>>> print(hb_read("data.hb")) # read a hb file
|
| 502 |
+
(0, 0) 1.0
|
| 503 |
+
(1, 1) 1.0
|
| 504 |
+
(2, 2) 1.0
|
| 505 |
+
|
| 506 |
+
"""
|
| 507 |
+
def _get_matrix(fid):
|
| 508 |
+
hb = HBFile(fid)
|
| 509 |
+
return hb.read_matrix()
|
| 510 |
+
|
| 511 |
+
if hasattr(path_or_open_file, 'read'):
|
| 512 |
+
return _get_matrix(path_or_open_file)
|
| 513 |
+
else:
|
| 514 |
+
with open(path_or_open_file) as f:
|
| 515 |
+
return _get_matrix(f)
|
| 516 |
+
|
| 517 |
+
|
| 518 |
+
def hb_write(path_or_open_file, m, hb_info=None):
|
| 519 |
+
"""Write HB-format file.
|
| 520 |
+
|
| 521 |
+
Parameters
|
| 522 |
+
----------
|
| 523 |
+
path_or_open_file : path-like or file-like
|
| 524 |
+
If a file-like object, it is used as-is. Otherwise, it is opened
|
| 525 |
+
before writing.
|
| 526 |
+
m : sparse-matrix
|
| 527 |
+
the sparse matrix to write
|
| 528 |
+
hb_info : HBInfo
|
| 529 |
+
contains the meta-data for write
|
| 530 |
+
|
| 531 |
+
Returns
|
| 532 |
+
-------
|
| 533 |
+
None
|
| 534 |
+
|
| 535 |
+
Notes
|
| 536 |
+
-----
|
| 537 |
+
At the moment not the full Harwell-Boeing format is supported. Supported
|
| 538 |
+
features are:
|
| 539 |
+
|
| 540 |
+
- assembled, non-symmetric, real matrices
|
| 541 |
+
- integer for pointer/indices
|
| 542 |
+
- exponential format for float values, and int format
|
| 543 |
+
|
| 544 |
+
Examples
|
| 545 |
+
--------
|
| 546 |
+
We can read and write a harwell-boeing format file:
|
| 547 |
+
|
| 548 |
+
>>> from scipy.io import hb_read, hb_write
|
| 549 |
+
>>> from scipy.sparse import csr_matrix, eye
|
| 550 |
+
>>> data = csr_matrix(eye(3)) # create a sparse matrix
|
| 551 |
+
>>> hb_write("data.hb", data) # write a hb file
|
| 552 |
+
>>> print(hb_read("data.hb")) # read a hb file
|
| 553 |
+
(0, 0) 1.0
|
| 554 |
+
(1, 1) 1.0
|
| 555 |
+
(2, 2) 1.0
|
| 556 |
+
|
| 557 |
+
"""
|
| 558 |
+
m = m.tocsc(copy=False)
|
| 559 |
+
|
| 560 |
+
if hb_info is None:
|
| 561 |
+
hb_info = HBInfo.from_data(m)
|
| 562 |
+
|
| 563 |
+
def _set_matrix(fid):
|
| 564 |
+
hb = HBFile(fid, hb_info)
|
| 565 |
+
return hb.write_matrix(m)
|
| 566 |
+
|
| 567 |
+
if hasattr(path_or_open_file, 'write'):
|
| 568 |
+
return _set_matrix(path_or_open_file)
|
| 569 |
+
else:
|
| 570 |
+
with open(path_or_open_file, 'w') as f:
|
| 571 |
+
return _set_matrix(f)
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__init__.py
ADDED
|
File without changes
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__pycache__/__init__.cpython-310.pyc
ADDED
|
Binary file (186 Bytes). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__pycache__/test_fortran_format.cpython-310.pyc
ADDED
|
Binary file (4.25 kB). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/__pycache__/test_hb.cpython-310.pyc
ADDED
|
Binary file (2.91 kB). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/test_fortran_format.py
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import numpy as np
|
| 2 |
+
|
| 3 |
+
from numpy.testing import assert_equal
|
| 4 |
+
from pytest import raises as assert_raises
|
| 5 |
+
|
| 6 |
+
from scipy.io._harwell_boeing import (
|
| 7 |
+
FortranFormatParser, IntFormat, ExpFormat, BadFortranFormat)
|
| 8 |
+
|
| 9 |
+
|
| 10 |
+
class TestFortranFormatParser:
|
| 11 |
+
def setup_method(self):
|
| 12 |
+
self.parser = FortranFormatParser()
|
| 13 |
+
|
| 14 |
+
def _test_equal(self, format, ref):
|
| 15 |
+
ret = self.parser.parse(format)
|
| 16 |
+
assert_equal(ret.__dict__, ref.__dict__)
|
| 17 |
+
|
| 18 |
+
def test_simple_int(self):
|
| 19 |
+
self._test_equal("(I4)", IntFormat(4))
|
| 20 |
+
|
| 21 |
+
def test_simple_repeated_int(self):
|
| 22 |
+
self._test_equal("(3I4)", IntFormat(4, repeat=3))
|
| 23 |
+
|
| 24 |
+
def test_simple_exp(self):
|
| 25 |
+
self._test_equal("(E4.3)", ExpFormat(4, 3))
|
| 26 |
+
|
| 27 |
+
def test_exp_exp(self):
|
| 28 |
+
self._test_equal("(E8.3E3)", ExpFormat(8, 3, 3))
|
| 29 |
+
|
| 30 |
+
def test_repeat_exp(self):
|
| 31 |
+
self._test_equal("(2E4.3)", ExpFormat(4, 3, repeat=2))
|
| 32 |
+
|
| 33 |
+
def test_repeat_exp_exp(self):
|
| 34 |
+
self._test_equal("(2E8.3E3)", ExpFormat(8, 3, 3, repeat=2))
|
| 35 |
+
|
| 36 |
+
def test_wrong_formats(self):
|
| 37 |
+
def _test_invalid(bad_format):
|
| 38 |
+
assert_raises(BadFortranFormat, lambda: self.parser.parse(bad_format))
|
| 39 |
+
_test_invalid("I4")
|
| 40 |
+
_test_invalid("(E4)")
|
| 41 |
+
_test_invalid("(E4.)")
|
| 42 |
+
_test_invalid("(E4.E3)")
|
| 43 |
+
|
| 44 |
+
|
| 45 |
+
class TestIntFormat:
|
| 46 |
+
def test_to_fortran(self):
|
| 47 |
+
f = [IntFormat(10), IntFormat(12, 10), IntFormat(12, 10, 3)]
|
| 48 |
+
res = ["(I10)", "(I12.10)", "(3I12.10)"]
|
| 49 |
+
|
| 50 |
+
for i, j in zip(f, res):
|
| 51 |
+
assert_equal(i.fortran_format, j)
|
| 52 |
+
|
| 53 |
+
def test_from_number(self):
|
| 54 |
+
f = [10, -12, 123456789]
|
| 55 |
+
r_f = [IntFormat(3, repeat=26), IntFormat(4, repeat=20),
|
| 56 |
+
IntFormat(10, repeat=8)]
|
| 57 |
+
for i, j in zip(f, r_f):
|
| 58 |
+
assert_equal(IntFormat.from_number(i).__dict__, j.__dict__)
|
| 59 |
+
|
| 60 |
+
|
| 61 |
+
class TestExpFormat:
|
| 62 |
+
def test_to_fortran(self):
|
| 63 |
+
f = [ExpFormat(10, 5), ExpFormat(12, 10), ExpFormat(12, 10, min=3),
|
| 64 |
+
ExpFormat(10, 5, repeat=3)]
|
| 65 |
+
res = ["(E10.5)", "(E12.10)", "(E12.10E3)", "(3E10.5)"]
|
| 66 |
+
|
| 67 |
+
for i, j in zip(f, res):
|
| 68 |
+
assert_equal(i.fortran_format, j)
|
| 69 |
+
|
| 70 |
+
def test_from_number(self):
|
| 71 |
+
f = np.array([1.0, -1.2])
|
| 72 |
+
r_f = [ExpFormat(24, 16, repeat=3), ExpFormat(25, 16, repeat=3)]
|
| 73 |
+
for i, j in zip(f, r_f):
|
| 74 |
+
assert_equal(ExpFormat.from_number(i).__dict__, j.__dict__)
|
videochat2/lib/python3.10/site-packages/scipy/io/_harwell_boeing/tests/test_hb.py
ADDED
|
@@ -0,0 +1,65 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from io import StringIO
|
| 2 |
+
import tempfile
|
| 3 |
+
|
| 4 |
+
import numpy as np
|
| 5 |
+
|
| 6 |
+
from numpy.testing import assert_equal, \
|
| 7 |
+
assert_array_almost_equal_nulp
|
| 8 |
+
|
| 9 |
+
from scipy.sparse import coo_matrix, csc_matrix, rand
|
| 10 |
+
|
| 11 |
+
from scipy.io import hb_read, hb_write
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
SIMPLE = """\
|
| 15 |
+
No Title |No Key
|
| 16 |
+
9 4 1 4
|
| 17 |
+
RUA 100 100 10 0
|
| 18 |
+
(26I3) (26I3) (3E23.15)
|
| 19 |
+
1 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
|
| 20 |
+
3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
|
| 21 |
+
3 3 3 3 3 3 3 4 4 4 6 6 6 6 6 6 6 6 6 6 6 8 9 9 9 9
|
| 22 |
+
9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 11
|
| 23 |
+
37 71 89 18 30 45 70 19 25 52
|
| 24 |
+
2.971243799687726e-01 3.662366682877375e-01 4.786962174699534e-01
|
| 25 |
+
6.490068647991184e-01 6.617490424831662e-02 8.870370343191623e-01
|
| 26 |
+
4.196478590163001e-01 5.649603072111251e-01 9.934423887087086e-01
|
| 27 |
+
6.912334991524289e-01
|
| 28 |
+
"""
|
| 29 |
+
|
| 30 |
+
SIMPLE_MATRIX = coo_matrix(
|
| 31 |
+
((0.297124379969, 0.366236668288, 0.47869621747, 0.649006864799,
|
| 32 |
+
0.0661749042483, 0.887037034319, 0.419647859016,
|
| 33 |
+
0.564960307211, 0.993442388709, 0.691233499152,),
|
| 34 |
+
(np.array([[36, 70, 88, 17, 29, 44, 69, 18, 24, 51],
|
| 35 |
+
[0, 4, 58, 61, 61, 72, 72, 73, 99, 99]]))))
|
| 36 |
+
|
| 37 |
+
|
| 38 |
+
def assert_csc_almost_equal(r, l):
|
| 39 |
+
r = csc_matrix(r)
|
| 40 |
+
l = csc_matrix(l)
|
| 41 |
+
assert_equal(r.indptr, l.indptr)
|
| 42 |
+
assert_equal(r.indices, l.indices)
|
| 43 |
+
assert_array_almost_equal_nulp(r.data, l.data, 10000)
|
| 44 |
+
|
| 45 |
+
|
| 46 |
+
class TestHBReader:
|
| 47 |
+
def test_simple(self):
|
| 48 |
+
m = hb_read(StringIO(SIMPLE))
|
| 49 |
+
assert_csc_almost_equal(m, SIMPLE_MATRIX)
|
| 50 |
+
|
| 51 |
+
|
| 52 |
+
class TestHBReadWrite:
|
| 53 |
+
|
| 54 |
+
def check_save_load(self, value):
|
| 55 |
+
with tempfile.NamedTemporaryFile(mode='w+t') as file:
|
| 56 |
+
hb_write(file, value)
|
| 57 |
+
file.file.seek(0)
|
| 58 |
+
value_loaded = hb_read(file)
|
| 59 |
+
assert_csc_almost_equal(value, value_loaded)
|
| 60 |
+
|
| 61 |
+
def test_simple(self):
|
| 62 |
+
random_matrix = rand(10, 100, 0.1)
|
| 63 |
+
for matrix_format in ('coo', 'csc', 'csr', 'bsr', 'dia', 'dok', 'lil'):
|
| 64 |
+
matrix = random_matrix.asformat(matrix_format, copy=False)
|
| 65 |
+
self.check_save_load(matrix)
|
videochat2/lib/python3.10/site-packages/scipy/io/_idl.py
ADDED
|
@@ -0,0 +1,918 @@
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|
| 1 |
+
# IDLSave - a python module to read IDL 'save' files
|
| 2 |
+
# Copyright (c) 2010 Thomas P. Robitaille
|
| 3 |
+
|
| 4 |
+
# Many thanks to Craig Markwardt for publishing the Unofficial Format
|
| 5 |
+
# Specification for IDL .sav files, without which this Python module would not
|
| 6 |
+
# exist (http://cow.physics.wisc.edu/~craigm/idl/savefmt).
|
| 7 |
+
|
| 8 |
+
# This code was developed by with permission from ITT Visual Information
|
| 9 |
+
# Systems. IDL(r) is a registered trademark of ITT Visual Information Systems,
|
| 10 |
+
# Inc. for their Interactive Data Language software.
|
| 11 |
+
|
| 12 |
+
# Permission is hereby granted, free of charge, to any person obtaining a
|
| 13 |
+
# copy of this software and associated documentation files (the "Software"),
|
| 14 |
+
# to deal in the Software without restriction, including without limitation
|
| 15 |
+
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
|
| 16 |
+
# and/or sell copies of the Software, and to permit persons to whom the
|
| 17 |
+
# Software is furnished to do so, subject to the following conditions:
|
| 18 |
+
|
| 19 |
+
# The above copyright notice and this permission notice shall be included in
|
| 20 |
+
# all copies or substantial portions of the Software.
|
| 21 |
+
|
| 22 |
+
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
| 23 |
+
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
| 24 |
+
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
| 25 |
+
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
| 26 |
+
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
| 27 |
+
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
|
| 28 |
+
# DEALINGS IN THE SOFTWARE.
|
| 29 |
+
|
| 30 |
+
__all__ = ['readsav']
|
| 31 |
+
|
| 32 |
+
import struct
|
| 33 |
+
import numpy as np
|
| 34 |
+
import tempfile
|
| 35 |
+
import zlib
|
| 36 |
+
import warnings
|
| 37 |
+
|
| 38 |
+
# Define the different data types that can be found in an IDL save file
|
| 39 |
+
DTYPE_DICT = {1: '>u1',
|
| 40 |
+
2: '>i2',
|
| 41 |
+
3: '>i4',
|
| 42 |
+
4: '>f4',
|
| 43 |
+
5: '>f8',
|
| 44 |
+
6: '>c8',
|
| 45 |
+
7: '|O',
|
| 46 |
+
8: '|O',
|
| 47 |
+
9: '>c16',
|
| 48 |
+
10: '|O',
|
| 49 |
+
11: '|O',
|
| 50 |
+
12: '>u2',
|
| 51 |
+
13: '>u4',
|
| 52 |
+
14: '>i8',
|
| 53 |
+
15: '>u8'}
|
| 54 |
+
|
| 55 |
+
# Define the different record types that can be found in an IDL save file
|
| 56 |
+
RECTYPE_DICT = {0: "START_MARKER",
|
| 57 |
+
1: "COMMON_VARIABLE",
|
| 58 |
+
2: "VARIABLE",
|
| 59 |
+
3: "SYSTEM_VARIABLE",
|
| 60 |
+
6: "END_MARKER",
|
| 61 |
+
10: "TIMESTAMP",
|
| 62 |
+
12: "COMPILED",
|
| 63 |
+
13: "IDENTIFICATION",
|
| 64 |
+
14: "VERSION",
|
| 65 |
+
15: "HEAP_HEADER",
|
| 66 |
+
16: "HEAP_DATA",
|
| 67 |
+
17: "PROMOTE64",
|
| 68 |
+
19: "NOTICE",
|
| 69 |
+
20: "DESCRIPTION"}
|
| 70 |
+
|
| 71 |
+
# Define a dictionary to contain structure definitions
|
| 72 |
+
STRUCT_DICT = {}
|
| 73 |
+
|
| 74 |
+
|
| 75 |
+
def _align_32(f):
|
| 76 |
+
'''Align to the next 32-bit position in a file'''
|
| 77 |
+
|
| 78 |
+
pos = f.tell()
|
| 79 |
+
if pos % 4 != 0:
|
| 80 |
+
f.seek(pos + 4 - pos % 4)
|
| 81 |
+
return
|
| 82 |
+
|
| 83 |
+
|
| 84 |
+
def _skip_bytes(f, n):
|
| 85 |
+
'''Skip `n` bytes'''
|
| 86 |
+
f.read(n)
|
| 87 |
+
return
|
| 88 |
+
|
| 89 |
+
|
| 90 |
+
def _read_bytes(f, n):
|
| 91 |
+
'''Read the next `n` bytes'''
|
| 92 |
+
return f.read(n)
|
| 93 |
+
|
| 94 |
+
|
| 95 |
+
def _read_byte(f):
|
| 96 |
+
'''Read a single byte'''
|
| 97 |
+
return np.uint8(struct.unpack('>B', f.read(4)[:1])[0])
|
| 98 |
+
|
| 99 |
+
|
| 100 |
+
def _read_long(f):
|
| 101 |
+
'''Read a signed 32-bit integer'''
|
| 102 |
+
return np.int32(struct.unpack('>l', f.read(4))[0])
|
| 103 |
+
|
| 104 |
+
|
| 105 |
+
def _read_int16(f):
|
| 106 |
+
'''Read a signed 16-bit integer'''
|
| 107 |
+
return np.int16(struct.unpack('>h', f.read(4)[2:4])[0])
|
| 108 |
+
|
| 109 |
+
|
| 110 |
+
def _read_int32(f):
|
| 111 |
+
'''Read a signed 32-bit integer'''
|
| 112 |
+
return np.int32(struct.unpack('>i', f.read(4))[0])
|
| 113 |
+
|
| 114 |
+
|
| 115 |
+
def _read_int64(f):
|
| 116 |
+
'''Read a signed 64-bit integer'''
|
| 117 |
+
return np.int64(struct.unpack('>q', f.read(8))[0])
|
| 118 |
+
|
| 119 |
+
|
| 120 |
+
def _read_uint16(f):
|
| 121 |
+
'''Read an unsigned 16-bit integer'''
|
| 122 |
+
return np.uint16(struct.unpack('>H', f.read(4)[2:4])[0])
|
| 123 |
+
|
| 124 |
+
|
| 125 |
+
def _read_uint32(f):
|
| 126 |
+
'''Read an unsigned 32-bit integer'''
|
| 127 |
+
return np.uint32(struct.unpack('>I', f.read(4))[0])
|
| 128 |
+
|
| 129 |
+
|
| 130 |
+
def _read_uint64(f):
|
| 131 |
+
'''Read an unsigned 64-bit integer'''
|
| 132 |
+
return np.uint64(struct.unpack('>Q', f.read(8))[0])
|
| 133 |
+
|
| 134 |
+
|
| 135 |
+
def _read_float32(f):
|
| 136 |
+
'''Read a 32-bit float'''
|
| 137 |
+
return np.float32(struct.unpack('>f', f.read(4))[0])
|
| 138 |
+
|
| 139 |
+
|
| 140 |
+
def _read_float64(f):
|
| 141 |
+
'''Read a 64-bit float'''
|
| 142 |
+
return np.float64(struct.unpack('>d', f.read(8))[0])
|
| 143 |
+
|
| 144 |
+
|
| 145 |
+
class Pointer:
|
| 146 |
+
'''Class used to define pointers'''
|
| 147 |
+
|
| 148 |
+
def __init__(self, index):
|
| 149 |
+
self.index = index
|
| 150 |
+
return
|
| 151 |
+
|
| 152 |
+
|
| 153 |
+
class ObjectPointer(Pointer):
|
| 154 |
+
'''Class used to define object pointers'''
|
| 155 |
+
pass
|
| 156 |
+
|
| 157 |
+
|
| 158 |
+
def _read_string(f):
|
| 159 |
+
'''Read a string'''
|
| 160 |
+
length = _read_long(f)
|
| 161 |
+
if length > 0:
|
| 162 |
+
chars = _read_bytes(f, length).decode('latin1')
|
| 163 |
+
_align_32(f)
|
| 164 |
+
else:
|
| 165 |
+
chars = ''
|
| 166 |
+
return chars
|
| 167 |
+
|
| 168 |
+
|
| 169 |
+
def _read_string_data(f):
|
| 170 |
+
'''Read a data string (length is specified twice)'''
|
| 171 |
+
length = _read_long(f)
|
| 172 |
+
if length > 0:
|
| 173 |
+
length = _read_long(f)
|
| 174 |
+
string_data = _read_bytes(f, length)
|
| 175 |
+
_align_32(f)
|
| 176 |
+
else:
|
| 177 |
+
string_data = ''
|
| 178 |
+
return string_data
|
| 179 |
+
|
| 180 |
+
|
| 181 |
+
def _read_data(f, dtype):
|
| 182 |
+
'''Read a variable with a specified data type'''
|
| 183 |
+
if dtype == 1:
|
| 184 |
+
if _read_int32(f) != 1:
|
| 185 |
+
raise Exception("Error occurred while reading byte variable")
|
| 186 |
+
return _read_byte(f)
|
| 187 |
+
elif dtype == 2:
|
| 188 |
+
return _read_int16(f)
|
| 189 |
+
elif dtype == 3:
|
| 190 |
+
return _read_int32(f)
|
| 191 |
+
elif dtype == 4:
|
| 192 |
+
return _read_float32(f)
|
| 193 |
+
elif dtype == 5:
|
| 194 |
+
return _read_float64(f)
|
| 195 |
+
elif dtype == 6:
|
| 196 |
+
real = _read_float32(f)
|
| 197 |
+
imag = _read_float32(f)
|
| 198 |
+
return np.complex64(real + imag * 1j)
|
| 199 |
+
elif dtype == 7:
|
| 200 |
+
return _read_string_data(f)
|
| 201 |
+
elif dtype == 8:
|
| 202 |
+
raise Exception("Should not be here - please report this")
|
| 203 |
+
elif dtype == 9:
|
| 204 |
+
real = _read_float64(f)
|
| 205 |
+
imag = _read_float64(f)
|
| 206 |
+
return np.complex128(real + imag * 1j)
|
| 207 |
+
elif dtype == 10:
|
| 208 |
+
return Pointer(_read_int32(f))
|
| 209 |
+
elif dtype == 11:
|
| 210 |
+
return ObjectPointer(_read_int32(f))
|
| 211 |
+
elif dtype == 12:
|
| 212 |
+
return _read_uint16(f)
|
| 213 |
+
elif dtype == 13:
|
| 214 |
+
return _read_uint32(f)
|
| 215 |
+
elif dtype == 14:
|
| 216 |
+
return _read_int64(f)
|
| 217 |
+
elif dtype == 15:
|
| 218 |
+
return _read_uint64(f)
|
| 219 |
+
else:
|
| 220 |
+
raise Exception("Unknown IDL type: %i - please report this" % dtype)
|
| 221 |
+
|
| 222 |
+
|
| 223 |
+
def _read_structure(f, array_desc, struct_desc):
|
| 224 |
+
'''
|
| 225 |
+
Read a structure, with the array and structure descriptors given as
|
| 226 |
+
`array_desc` and `structure_desc` respectively.
|
| 227 |
+
'''
|
| 228 |
+
|
| 229 |
+
nrows = array_desc['nelements']
|
| 230 |
+
columns = struct_desc['tagtable']
|
| 231 |
+
|
| 232 |
+
dtype = []
|
| 233 |
+
for col in columns:
|
| 234 |
+
if col['structure'] or col['array']:
|
| 235 |
+
dtype.append(((col['name'].lower(), col['name']), np.object_))
|
| 236 |
+
else:
|
| 237 |
+
if col['typecode'] in DTYPE_DICT:
|
| 238 |
+
dtype.append(((col['name'].lower(), col['name']),
|
| 239 |
+
DTYPE_DICT[col['typecode']]))
|
| 240 |
+
else:
|
| 241 |
+
raise Exception("Variable type %i not implemented" %
|
| 242 |
+
col['typecode'])
|
| 243 |
+
|
| 244 |
+
structure = np.rec.recarray((nrows, ), dtype=dtype)
|
| 245 |
+
|
| 246 |
+
for i in range(nrows):
|
| 247 |
+
for col in columns:
|
| 248 |
+
dtype = col['typecode']
|
| 249 |
+
if col['structure']:
|
| 250 |
+
structure[col['name']][i] = _read_structure(f,
|
| 251 |
+
struct_desc['arrtable'][col['name']],
|
| 252 |
+
struct_desc['structtable'][col['name']])
|
| 253 |
+
elif col['array']:
|
| 254 |
+
structure[col['name']][i] = _read_array(f, dtype,
|
| 255 |
+
struct_desc['arrtable'][col['name']])
|
| 256 |
+
else:
|
| 257 |
+
structure[col['name']][i] = _read_data(f, dtype)
|
| 258 |
+
|
| 259 |
+
# Reshape structure if needed
|
| 260 |
+
if array_desc['ndims'] > 1:
|
| 261 |
+
dims = array_desc['dims'][:int(array_desc['ndims'])]
|
| 262 |
+
dims.reverse()
|
| 263 |
+
structure = structure.reshape(dims)
|
| 264 |
+
|
| 265 |
+
return structure
|
| 266 |
+
|
| 267 |
+
|
| 268 |
+
def _read_array(f, typecode, array_desc):
|
| 269 |
+
'''
|
| 270 |
+
Read an array of type `typecode`, with the array descriptor given as
|
| 271 |
+
`array_desc`.
|
| 272 |
+
'''
|
| 273 |
+
|
| 274 |
+
if typecode in [1, 3, 4, 5, 6, 9, 13, 14, 15]:
|
| 275 |
+
|
| 276 |
+
if typecode == 1:
|
| 277 |
+
nbytes = _read_int32(f)
|
| 278 |
+
if nbytes != array_desc['nbytes']:
|
| 279 |
+
warnings.warn("Not able to verify number of bytes from header",
|
| 280 |
+
stacklevel=3)
|
| 281 |
+
|
| 282 |
+
# Read bytes as numpy array
|
| 283 |
+
array = np.frombuffer(f.read(array_desc['nbytes']),
|
| 284 |
+
dtype=DTYPE_DICT[typecode])
|
| 285 |
+
|
| 286 |
+
elif typecode in [2, 12]:
|
| 287 |
+
|
| 288 |
+
# These are 2 byte types, need to skip every two as they are not packed
|
| 289 |
+
|
| 290 |
+
array = np.frombuffer(f.read(array_desc['nbytes']*2),
|
| 291 |
+
dtype=DTYPE_DICT[typecode])[1::2]
|
| 292 |
+
|
| 293 |
+
else:
|
| 294 |
+
|
| 295 |
+
# Read bytes into list
|
| 296 |
+
array = []
|
| 297 |
+
for i in range(array_desc['nelements']):
|
| 298 |
+
dtype = typecode
|
| 299 |
+
data = _read_data(f, dtype)
|
| 300 |
+
array.append(data)
|
| 301 |
+
|
| 302 |
+
array = np.array(array, dtype=np.object_)
|
| 303 |
+
|
| 304 |
+
# Reshape array if needed
|
| 305 |
+
if array_desc['ndims'] > 1:
|
| 306 |
+
dims = array_desc['dims'][:int(array_desc['ndims'])]
|
| 307 |
+
dims.reverse()
|
| 308 |
+
array = array.reshape(dims)
|
| 309 |
+
|
| 310 |
+
# Go to next alignment position
|
| 311 |
+
_align_32(f)
|
| 312 |
+
|
| 313 |
+
return array
|
| 314 |
+
|
| 315 |
+
|
| 316 |
+
def _read_record(f):
|
| 317 |
+
'''Function to read in a full record'''
|
| 318 |
+
|
| 319 |
+
record = {'rectype': _read_long(f)}
|
| 320 |
+
|
| 321 |
+
nextrec = _read_uint32(f)
|
| 322 |
+
nextrec += _read_uint32(f).astype(np.int64) * 2**32
|
| 323 |
+
|
| 324 |
+
_skip_bytes(f, 4)
|
| 325 |
+
|
| 326 |
+
if record['rectype'] not in RECTYPE_DICT:
|
| 327 |
+
raise Exception("Unknown RECTYPE: %i" % record['rectype'])
|
| 328 |
+
|
| 329 |
+
record['rectype'] = RECTYPE_DICT[record['rectype']]
|
| 330 |
+
|
| 331 |
+
if record['rectype'] in ["VARIABLE", "HEAP_DATA"]:
|
| 332 |
+
|
| 333 |
+
if record['rectype'] == "VARIABLE":
|
| 334 |
+
record['varname'] = _read_string(f)
|
| 335 |
+
else:
|
| 336 |
+
record['heap_index'] = _read_long(f)
|
| 337 |
+
_skip_bytes(f, 4)
|
| 338 |
+
|
| 339 |
+
rectypedesc = _read_typedesc(f)
|
| 340 |
+
|
| 341 |
+
if rectypedesc['typecode'] == 0:
|
| 342 |
+
|
| 343 |
+
if nextrec == f.tell():
|
| 344 |
+
record['data'] = None # Indicates NULL value
|
| 345 |
+
else:
|
| 346 |
+
raise ValueError("Unexpected type code: 0")
|
| 347 |
+
|
| 348 |
+
else:
|
| 349 |
+
|
| 350 |
+
varstart = _read_long(f)
|
| 351 |
+
if varstart != 7:
|
| 352 |
+
raise Exception("VARSTART is not 7")
|
| 353 |
+
|
| 354 |
+
if rectypedesc['structure']:
|
| 355 |
+
record['data'] = _read_structure(f, rectypedesc['array_desc'],
|
| 356 |
+
rectypedesc['struct_desc'])
|
| 357 |
+
elif rectypedesc['array']:
|
| 358 |
+
record['data'] = _read_array(f, rectypedesc['typecode'],
|
| 359 |
+
rectypedesc['array_desc'])
|
| 360 |
+
else:
|
| 361 |
+
dtype = rectypedesc['typecode']
|
| 362 |
+
record['data'] = _read_data(f, dtype)
|
| 363 |
+
|
| 364 |
+
elif record['rectype'] == "TIMESTAMP":
|
| 365 |
+
|
| 366 |
+
_skip_bytes(f, 4*256)
|
| 367 |
+
record['date'] = _read_string(f)
|
| 368 |
+
record['user'] = _read_string(f)
|
| 369 |
+
record['host'] = _read_string(f)
|
| 370 |
+
|
| 371 |
+
elif record['rectype'] == "VERSION":
|
| 372 |
+
|
| 373 |
+
record['format'] = _read_long(f)
|
| 374 |
+
record['arch'] = _read_string(f)
|
| 375 |
+
record['os'] = _read_string(f)
|
| 376 |
+
record['release'] = _read_string(f)
|
| 377 |
+
|
| 378 |
+
elif record['rectype'] == "IDENTIFICATON":
|
| 379 |
+
|
| 380 |
+
record['author'] = _read_string(f)
|
| 381 |
+
record['title'] = _read_string(f)
|
| 382 |
+
record['idcode'] = _read_string(f)
|
| 383 |
+
|
| 384 |
+
elif record['rectype'] == "NOTICE":
|
| 385 |
+
|
| 386 |
+
record['notice'] = _read_string(f)
|
| 387 |
+
|
| 388 |
+
elif record['rectype'] == "DESCRIPTION":
|
| 389 |
+
|
| 390 |
+
record['description'] = _read_string_data(f)
|
| 391 |
+
|
| 392 |
+
elif record['rectype'] == "HEAP_HEADER":
|
| 393 |
+
|
| 394 |
+
record['nvalues'] = _read_long(f)
|
| 395 |
+
record['indices'] = [_read_long(f) for _ in range(record['nvalues'])]
|
| 396 |
+
|
| 397 |
+
elif record['rectype'] == "COMMONBLOCK":
|
| 398 |
+
|
| 399 |
+
record['nvars'] = _read_long(f)
|
| 400 |
+
record['name'] = _read_string(f)
|
| 401 |
+
record['varnames'] = [_read_string(f) for _ in range(record['nvars'])]
|
| 402 |
+
|
| 403 |
+
elif record['rectype'] == "END_MARKER":
|
| 404 |
+
|
| 405 |
+
record['end'] = True
|
| 406 |
+
|
| 407 |
+
elif record['rectype'] == "UNKNOWN":
|
| 408 |
+
|
| 409 |
+
warnings.warn("Skipping UNKNOWN record", stacklevel=3)
|
| 410 |
+
|
| 411 |
+
elif record['rectype'] == "SYSTEM_VARIABLE":
|
| 412 |
+
|
| 413 |
+
warnings.warn("Skipping SYSTEM_VARIABLE record", stacklevel=3)
|
| 414 |
+
|
| 415 |
+
else:
|
| 416 |
+
|
| 417 |
+
raise Exception(f"record['rectype']={record['rectype']} not implemented")
|
| 418 |
+
|
| 419 |
+
f.seek(nextrec)
|
| 420 |
+
|
| 421 |
+
return record
|
| 422 |
+
|
| 423 |
+
|
| 424 |
+
def _read_typedesc(f):
|
| 425 |
+
'''Function to read in a type descriptor'''
|
| 426 |
+
|
| 427 |
+
typedesc = {'typecode': _read_long(f), 'varflags': _read_long(f)}
|
| 428 |
+
|
| 429 |
+
if typedesc['varflags'] & 2 == 2:
|
| 430 |
+
raise Exception("System variables not implemented")
|
| 431 |
+
|
| 432 |
+
typedesc['array'] = typedesc['varflags'] & 4 == 4
|
| 433 |
+
typedesc['structure'] = typedesc['varflags'] & 32 == 32
|
| 434 |
+
|
| 435 |
+
if typedesc['structure']:
|
| 436 |
+
typedesc['array_desc'] = _read_arraydesc(f)
|
| 437 |
+
typedesc['struct_desc'] = _read_structdesc(f)
|
| 438 |
+
elif typedesc['array']:
|
| 439 |
+
typedesc['array_desc'] = _read_arraydesc(f)
|
| 440 |
+
|
| 441 |
+
return typedesc
|
| 442 |
+
|
| 443 |
+
|
| 444 |
+
def _read_arraydesc(f):
|
| 445 |
+
'''Function to read in an array descriptor'''
|
| 446 |
+
|
| 447 |
+
arraydesc = {'arrstart': _read_long(f)}
|
| 448 |
+
|
| 449 |
+
if arraydesc['arrstart'] == 8:
|
| 450 |
+
|
| 451 |
+
_skip_bytes(f, 4)
|
| 452 |
+
|
| 453 |
+
arraydesc['nbytes'] = _read_long(f)
|
| 454 |
+
arraydesc['nelements'] = _read_long(f)
|
| 455 |
+
arraydesc['ndims'] = _read_long(f)
|
| 456 |
+
|
| 457 |
+
_skip_bytes(f, 8)
|
| 458 |
+
|
| 459 |
+
arraydesc['nmax'] = _read_long(f)
|
| 460 |
+
|
| 461 |
+
arraydesc['dims'] = [_read_long(f) for _ in range(arraydesc['nmax'])]
|
| 462 |
+
|
| 463 |
+
elif arraydesc['arrstart'] == 18:
|
| 464 |
+
|
| 465 |
+
warnings.warn("Using experimental 64-bit array read", stacklevel=3)
|
| 466 |
+
|
| 467 |
+
_skip_bytes(f, 8)
|
| 468 |
+
|
| 469 |
+
arraydesc['nbytes'] = _read_uint64(f)
|
| 470 |
+
arraydesc['nelements'] = _read_uint64(f)
|
| 471 |
+
arraydesc['ndims'] = _read_long(f)
|
| 472 |
+
|
| 473 |
+
_skip_bytes(f, 8)
|
| 474 |
+
|
| 475 |
+
arraydesc['nmax'] = 8
|
| 476 |
+
|
| 477 |
+
arraydesc['dims'] = []
|
| 478 |
+
for d in range(arraydesc['nmax']):
|
| 479 |
+
v = _read_long(f)
|
| 480 |
+
if v != 0:
|
| 481 |
+
raise Exception("Expected a zero in ARRAY_DESC")
|
| 482 |
+
arraydesc['dims'].append(_read_long(f))
|
| 483 |
+
|
| 484 |
+
else:
|
| 485 |
+
|
| 486 |
+
raise Exception("Unknown ARRSTART: %i" % arraydesc['arrstart'])
|
| 487 |
+
|
| 488 |
+
return arraydesc
|
| 489 |
+
|
| 490 |
+
|
| 491 |
+
def _read_structdesc(f):
|
| 492 |
+
'''Function to read in a structure descriptor'''
|
| 493 |
+
|
| 494 |
+
structdesc = {}
|
| 495 |
+
|
| 496 |
+
structstart = _read_long(f)
|
| 497 |
+
if structstart != 9:
|
| 498 |
+
raise Exception("STRUCTSTART should be 9")
|
| 499 |
+
|
| 500 |
+
structdesc['name'] = _read_string(f)
|
| 501 |
+
predef = _read_long(f)
|
| 502 |
+
structdesc['ntags'] = _read_long(f)
|
| 503 |
+
structdesc['nbytes'] = _read_long(f)
|
| 504 |
+
|
| 505 |
+
structdesc['predef'] = predef & 1
|
| 506 |
+
structdesc['inherits'] = predef & 2
|
| 507 |
+
structdesc['is_super'] = predef & 4
|
| 508 |
+
|
| 509 |
+
if not structdesc['predef']:
|
| 510 |
+
|
| 511 |
+
structdesc['tagtable'] = [_read_tagdesc(f)
|
| 512 |
+
for _ in range(structdesc['ntags'])]
|
| 513 |
+
|
| 514 |
+
for tag in structdesc['tagtable']:
|
| 515 |
+
tag['name'] = _read_string(f)
|
| 516 |
+
|
| 517 |
+
structdesc['arrtable'] = {tag['name']: _read_arraydesc(f)
|
| 518 |
+
for tag in structdesc['tagtable']
|
| 519 |
+
if tag['array']}
|
| 520 |
+
|
| 521 |
+
structdesc['structtable'] = {tag['name']: _read_structdesc(f)
|
| 522 |
+
for tag in structdesc['tagtable']
|
| 523 |
+
if tag['structure']}
|
| 524 |
+
|
| 525 |
+
if structdesc['inherits'] or structdesc['is_super']:
|
| 526 |
+
structdesc['classname'] = _read_string(f)
|
| 527 |
+
structdesc['nsupclasses'] = _read_long(f)
|
| 528 |
+
structdesc['supclassnames'] = [
|
| 529 |
+
_read_string(f) for _ in range(structdesc['nsupclasses'])]
|
| 530 |
+
structdesc['supclasstable'] = [
|
| 531 |
+
_read_structdesc(f) for _ in range(structdesc['nsupclasses'])]
|
| 532 |
+
|
| 533 |
+
STRUCT_DICT[structdesc['name']] = structdesc
|
| 534 |
+
|
| 535 |
+
else:
|
| 536 |
+
|
| 537 |
+
if structdesc['name'] not in STRUCT_DICT:
|
| 538 |
+
raise Exception("PREDEF=1 but can't find definition")
|
| 539 |
+
|
| 540 |
+
structdesc = STRUCT_DICT[structdesc['name']]
|
| 541 |
+
|
| 542 |
+
return structdesc
|
| 543 |
+
|
| 544 |
+
|
| 545 |
+
def _read_tagdesc(f):
|
| 546 |
+
'''Function to read in a tag descriptor'''
|
| 547 |
+
|
| 548 |
+
tagdesc = {'offset': _read_long(f)}
|
| 549 |
+
|
| 550 |
+
if tagdesc['offset'] == -1:
|
| 551 |
+
tagdesc['offset'] = _read_uint64(f)
|
| 552 |
+
|
| 553 |
+
tagdesc['typecode'] = _read_long(f)
|
| 554 |
+
tagflags = _read_long(f)
|
| 555 |
+
|
| 556 |
+
tagdesc['array'] = tagflags & 4 == 4
|
| 557 |
+
tagdesc['structure'] = tagflags & 32 == 32
|
| 558 |
+
tagdesc['scalar'] = tagdesc['typecode'] in DTYPE_DICT
|
| 559 |
+
# Assume '10'x is scalar
|
| 560 |
+
|
| 561 |
+
return tagdesc
|
| 562 |
+
|
| 563 |
+
|
| 564 |
+
def _replace_heap(variable, heap):
|
| 565 |
+
|
| 566 |
+
if isinstance(variable, Pointer):
|
| 567 |
+
|
| 568 |
+
while isinstance(variable, Pointer):
|
| 569 |
+
|
| 570 |
+
if variable.index == 0:
|
| 571 |
+
variable = None
|
| 572 |
+
else:
|
| 573 |
+
if variable.index in heap:
|
| 574 |
+
variable = heap[variable.index]
|
| 575 |
+
else:
|
| 576 |
+
warnings.warn("Variable referenced by pointer not found "
|
| 577 |
+
"in heap: variable will be set to None",
|
| 578 |
+
stacklevel=3)
|
| 579 |
+
variable = None
|
| 580 |
+
|
| 581 |
+
replace, new = _replace_heap(variable, heap)
|
| 582 |
+
|
| 583 |
+
if replace:
|
| 584 |
+
variable = new
|
| 585 |
+
|
| 586 |
+
return True, variable
|
| 587 |
+
|
| 588 |
+
elif isinstance(variable, np.rec.recarray):
|
| 589 |
+
|
| 590 |
+
# Loop over records
|
| 591 |
+
for ir, record in enumerate(variable):
|
| 592 |
+
|
| 593 |
+
replace, new = _replace_heap(record, heap)
|
| 594 |
+
|
| 595 |
+
if replace:
|
| 596 |
+
variable[ir] = new
|
| 597 |
+
|
| 598 |
+
return False, variable
|
| 599 |
+
|
| 600 |
+
elif isinstance(variable, np.record):
|
| 601 |
+
|
| 602 |
+
# Loop over values
|
| 603 |
+
for iv, value in enumerate(variable):
|
| 604 |
+
|
| 605 |
+
replace, new = _replace_heap(value, heap)
|
| 606 |
+
|
| 607 |
+
if replace:
|
| 608 |
+
variable[iv] = new
|
| 609 |
+
|
| 610 |
+
return False, variable
|
| 611 |
+
|
| 612 |
+
elif isinstance(variable, np.ndarray):
|
| 613 |
+
|
| 614 |
+
# Loop over values if type is np.object_
|
| 615 |
+
if variable.dtype.type is np.object_:
|
| 616 |
+
|
| 617 |
+
for iv in range(variable.size):
|
| 618 |
+
|
| 619 |
+
replace, new = _replace_heap(variable.item(iv), heap)
|
| 620 |
+
|
| 621 |
+
if replace:
|
| 622 |
+
variable.reshape(-1)[iv] = new
|
| 623 |
+
|
| 624 |
+
return False, variable
|
| 625 |
+
|
| 626 |
+
else:
|
| 627 |
+
|
| 628 |
+
return False, variable
|
| 629 |
+
|
| 630 |
+
|
| 631 |
+
class AttrDict(dict):
|
| 632 |
+
'''
|
| 633 |
+
A case-insensitive dictionary with access via item, attribute, and call
|
| 634 |
+
notations:
|
| 635 |
+
|
| 636 |
+
>>> from scipy.io._idl import AttrDict
|
| 637 |
+
>>> d = AttrDict()
|
| 638 |
+
>>> d['Variable'] = 123
|
| 639 |
+
>>> d['Variable']
|
| 640 |
+
123
|
| 641 |
+
>>> d.Variable
|
| 642 |
+
123
|
| 643 |
+
>>> d.variable
|
| 644 |
+
123
|
| 645 |
+
>>> d('VARIABLE')
|
| 646 |
+
123
|
| 647 |
+
>>> d['missing']
|
| 648 |
+
Traceback (most recent error last):
|
| 649 |
+
...
|
| 650 |
+
KeyError: 'missing'
|
| 651 |
+
>>> d.missing
|
| 652 |
+
Traceback (most recent error last):
|
| 653 |
+
...
|
| 654 |
+
AttributeError: 'AttrDict' object has no attribute 'missing'
|
| 655 |
+
'''
|
| 656 |
+
|
| 657 |
+
def __init__(self, init={}):
|
| 658 |
+
dict.__init__(self, init)
|
| 659 |
+
|
| 660 |
+
def __getitem__(self, name):
|
| 661 |
+
return super().__getitem__(name.lower())
|
| 662 |
+
|
| 663 |
+
def __setitem__(self, key, value):
|
| 664 |
+
return super().__setitem__(key.lower(), value)
|
| 665 |
+
|
| 666 |
+
def __getattr__(self, name):
|
| 667 |
+
try:
|
| 668 |
+
return self.__getitem__(name)
|
| 669 |
+
except KeyError:
|
| 670 |
+
raise AttributeError(
|
| 671 |
+
f"'{type(self)}' object has no attribute '{name}'") from None
|
| 672 |
+
|
| 673 |
+
__setattr__ = __setitem__
|
| 674 |
+
__call__ = __getitem__
|
| 675 |
+
|
| 676 |
+
|
| 677 |
+
def readsav(file_name, idict=None, python_dict=False,
|
| 678 |
+
uncompressed_file_name=None, verbose=False):
|
| 679 |
+
"""
|
| 680 |
+
Read an IDL .sav file.
|
| 681 |
+
|
| 682 |
+
Parameters
|
| 683 |
+
----------
|
| 684 |
+
file_name : str
|
| 685 |
+
Name of the IDL save file.
|
| 686 |
+
idict : dict, optional
|
| 687 |
+
Dictionary in which to insert .sav file variables.
|
| 688 |
+
python_dict : bool, optional
|
| 689 |
+
By default, the object return is not a Python dictionary, but a
|
| 690 |
+
case-insensitive dictionary with item, attribute, and call access
|
| 691 |
+
to variables. To get a standard Python dictionary, set this option
|
| 692 |
+
to True.
|
| 693 |
+
uncompressed_file_name : str, optional
|
| 694 |
+
This option only has an effect for .sav files written with the
|
| 695 |
+
/compress option. If a file name is specified, compressed .sav
|
| 696 |
+
files are uncompressed to this file. Otherwise, readsav will use
|
| 697 |
+
the `tempfile` module to determine a temporary filename
|
| 698 |
+
automatically, and will remove the temporary file upon successfully
|
| 699 |
+
reading it in.
|
| 700 |
+
verbose : bool, optional
|
| 701 |
+
Whether to print out information about the save file, including
|
| 702 |
+
the records read, and available variables.
|
| 703 |
+
|
| 704 |
+
Returns
|
| 705 |
+
-------
|
| 706 |
+
idl_dict : AttrDict or dict
|
| 707 |
+
If `python_dict` is set to False (default), this function returns a
|
| 708 |
+
case-insensitive dictionary with item, attribute, and call access
|
| 709 |
+
to variables. If `python_dict` is set to True, this function
|
| 710 |
+
returns a Python dictionary with all variable names in lowercase.
|
| 711 |
+
If `idict` was specified, then variables are written to the
|
| 712 |
+
dictionary specified, and the updated dictionary is returned.
|
| 713 |
+
|
| 714 |
+
Examples
|
| 715 |
+
--------
|
| 716 |
+
>>> from os.path import dirname, join as pjoin
|
| 717 |
+
>>> import scipy.io as sio
|
| 718 |
+
>>> from scipy.io import readsav
|
| 719 |
+
|
| 720 |
+
Get the filename for an example .sav file from the tests/data directory.
|
| 721 |
+
|
| 722 |
+
>>> data_dir = pjoin(dirname(sio.__file__), 'tests', 'data')
|
| 723 |
+
>>> sav_fname = pjoin(data_dir, 'array_float32_1d.sav')
|
| 724 |
+
|
| 725 |
+
Load the .sav file contents.
|
| 726 |
+
|
| 727 |
+
>>> sav_data = readsav(sav_fname)
|
| 728 |
+
|
| 729 |
+
Get keys of the .sav file contents.
|
| 730 |
+
|
| 731 |
+
>>> print(sav_data.keys())
|
| 732 |
+
dict_keys(['array1d'])
|
| 733 |
+
|
| 734 |
+
Access a content with a key.
|
| 735 |
+
|
| 736 |
+
>>> print(sav_data['array1d'])
|
| 737 |
+
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
|
| 738 |
+
0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
|
| 739 |
+
0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
|
| 740 |
+
0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
|
| 741 |
+
0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
|
| 742 |
+
0. 0. 0.]
|
| 743 |
+
|
| 744 |
+
"""
|
| 745 |
+
|
| 746 |
+
# Initialize record and variable holders
|
| 747 |
+
records = []
|
| 748 |
+
if python_dict or idict:
|
| 749 |
+
variables = {}
|
| 750 |
+
else:
|
| 751 |
+
variables = AttrDict()
|
| 752 |
+
|
| 753 |
+
# Open the IDL file
|
| 754 |
+
f = open(file_name, 'rb')
|
| 755 |
+
|
| 756 |
+
# Read the signature, which should be 'SR'
|
| 757 |
+
signature = _read_bytes(f, 2)
|
| 758 |
+
if signature != b'SR':
|
| 759 |
+
raise Exception("Invalid SIGNATURE: %s" % signature)
|
| 760 |
+
|
| 761 |
+
# Next, the record format, which is '\x00\x04' for normal .sav
|
| 762 |
+
# files, and '\x00\x06' for compressed .sav files.
|
| 763 |
+
recfmt = _read_bytes(f, 2)
|
| 764 |
+
|
| 765 |
+
if recfmt == b'\x00\x04':
|
| 766 |
+
pass
|
| 767 |
+
|
| 768 |
+
elif recfmt == b'\x00\x06':
|
| 769 |
+
|
| 770 |
+
if verbose:
|
| 771 |
+
print("IDL Save file is compressed")
|
| 772 |
+
|
| 773 |
+
if uncompressed_file_name:
|
| 774 |
+
fout = open(uncompressed_file_name, 'w+b')
|
| 775 |
+
else:
|
| 776 |
+
fout = tempfile.NamedTemporaryFile(suffix='.sav')
|
| 777 |
+
|
| 778 |
+
if verbose:
|
| 779 |
+
print(" -> expanding to %s" % fout.name)
|
| 780 |
+
|
| 781 |
+
# Write header
|
| 782 |
+
fout.write(b'SR\x00\x04')
|
| 783 |
+
|
| 784 |
+
# Cycle through records
|
| 785 |
+
while True:
|
| 786 |
+
|
| 787 |
+
# Read record type
|
| 788 |
+
rectype = _read_long(f)
|
| 789 |
+
fout.write(struct.pack('>l', int(rectype)))
|
| 790 |
+
|
| 791 |
+
# Read position of next record and return as int
|
| 792 |
+
nextrec = _read_uint32(f)
|
| 793 |
+
nextrec += _read_uint32(f).astype(np.int64) * 2**32
|
| 794 |
+
|
| 795 |
+
# Read the unknown 4 bytes
|
| 796 |
+
unknown = f.read(4)
|
| 797 |
+
|
| 798 |
+
# Check if the end of the file has been reached
|
| 799 |
+
if RECTYPE_DICT[rectype] == 'END_MARKER':
|
| 800 |
+
modval = np.int64(2**32)
|
| 801 |
+
fout.write(struct.pack('>I', int(nextrec) % modval))
|
| 802 |
+
fout.write(
|
| 803 |
+
struct.pack('>I', int((nextrec - (nextrec % modval)) / modval))
|
| 804 |
+
)
|
| 805 |
+
fout.write(unknown)
|
| 806 |
+
break
|
| 807 |
+
|
| 808 |
+
# Find current position
|
| 809 |
+
pos = f.tell()
|
| 810 |
+
|
| 811 |
+
# Decompress record
|
| 812 |
+
rec_string = zlib.decompress(f.read(nextrec-pos))
|
| 813 |
+
|
| 814 |
+
# Find new position of next record
|
| 815 |
+
nextrec = fout.tell() + len(rec_string) + 12
|
| 816 |
+
|
| 817 |
+
# Write out record
|
| 818 |
+
fout.write(struct.pack('>I', int(nextrec % 2**32)))
|
| 819 |
+
fout.write(struct.pack('>I', int((nextrec - (nextrec % 2**32)) / 2**32)))
|
| 820 |
+
fout.write(unknown)
|
| 821 |
+
fout.write(rec_string)
|
| 822 |
+
|
| 823 |
+
# Close the original compressed file
|
| 824 |
+
f.close()
|
| 825 |
+
|
| 826 |
+
# Set f to be the decompressed file, and skip the first four bytes
|
| 827 |
+
f = fout
|
| 828 |
+
f.seek(4)
|
| 829 |
+
|
| 830 |
+
else:
|
| 831 |
+
raise Exception("Invalid RECFMT: %s" % recfmt)
|
| 832 |
+
|
| 833 |
+
# Loop through records, and add them to the list
|
| 834 |
+
while True:
|
| 835 |
+
r = _read_record(f)
|
| 836 |
+
records.append(r)
|
| 837 |
+
if 'end' in r:
|
| 838 |
+
if r['end']:
|
| 839 |
+
break
|
| 840 |
+
|
| 841 |
+
# Close the file
|
| 842 |
+
f.close()
|
| 843 |
+
|
| 844 |
+
# Find heap data variables
|
| 845 |
+
heap = {}
|
| 846 |
+
for r in records:
|
| 847 |
+
if r['rectype'] == "HEAP_DATA":
|
| 848 |
+
heap[r['heap_index']] = r['data']
|
| 849 |
+
|
| 850 |
+
# Find all variables
|
| 851 |
+
for r in records:
|
| 852 |
+
if r['rectype'] == "VARIABLE":
|
| 853 |
+
replace, new = _replace_heap(r['data'], heap)
|
| 854 |
+
if replace:
|
| 855 |
+
r['data'] = new
|
| 856 |
+
variables[r['varname'].lower()] = r['data']
|
| 857 |
+
|
| 858 |
+
if verbose:
|
| 859 |
+
|
| 860 |
+
# Print out timestamp info about the file
|
| 861 |
+
for record in records:
|
| 862 |
+
if record['rectype'] == "TIMESTAMP":
|
| 863 |
+
print("-"*50)
|
| 864 |
+
print("Date: %s" % record['date'])
|
| 865 |
+
print("User: %s" % record['user'])
|
| 866 |
+
print("Host: %s" % record['host'])
|
| 867 |
+
break
|
| 868 |
+
|
| 869 |
+
# Print out version info about the file
|
| 870 |
+
for record in records:
|
| 871 |
+
if record['rectype'] == "VERSION":
|
| 872 |
+
print("-"*50)
|
| 873 |
+
print("Format: %s" % record['format'])
|
| 874 |
+
print("Architecture: %s" % record['arch'])
|
| 875 |
+
print("Operating System: %s" % record['os'])
|
| 876 |
+
print("IDL Version: %s" % record['release'])
|
| 877 |
+
break
|
| 878 |
+
|
| 879 |
+
# Print out identification info about the file
|
| 880 |
+
for record in records:
|
| 881 |
+
if record['rectype'] == "IDENTIFICATON":
|
| 882 |
+
print("-"*50)
|
| 883 |
+
print("Author: %s" % record['author'])
|
| 884 |
+
print("Title: %s" % record['title'])
|
| 885 |
+
print("ID Code: %s" % record['idcode'])
|
| 886 |
+
break
|
| 887 |
+
|
| 888 |
+
# Print out descriptions saved with the file
|
| 889 |
+
for record in records:
|
| 890 |
+
if record['rectype'] == "DESCRIPTION":
|
| 891 |
+
print("-"*50)
|
| 892 |
+
print("Description: %s" % record['description'])
|
| 893 |
+
break
|
| 894 |
+
|
| 895 |
+
print("-"*50)
|
| 896 |
+
print("Successfully read %i records of which:" %
|
| 897 |
+
(len(records)))
|
| 898 |
+
|
| 899 |
+
# Create convenience list of record types
|
| 900 |
+
rectypes = [r['rectype'] for r in records]
|
| 901 |
+
|
| 902 |
+
for rt in set(rectypes):
|
| 903 |
+
if rt != 'END_MARKER':
|
| 904 |
+
print(" - %i are of type %s" % (rectypes.count(rt), rt))
|
| 905 |
+
print("-"*50)
|
| 906 |
+
|
| 907 |
+
if 'VARIABLE' in rectypes:
|
| 908 |
+
print("Available variables:")
|
| 909 |
+
for var in variables:
|
| 910 |
+
print(f" - {var} [{type(variables[var])}]")
|
| 911 |
+
print("-"*50)
|
| 912 |
+
|
| 913 |
+
if idict:
|
| 914 |
+
for var in variables:
|
| 915 |
+
idict[var] = variables[var]
|
| 916 |
+
return idict
|
| 917 |
+
else:
|
| 918 |
+
return variables
|
videochat2/lib/python3.10/site-packages/scipy/io/_mmio.py
ADDED
|
@@ -0,0 +1,961 @@
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|
| 1 |
+
"""
|
| 2 |
+
Matrix Market I/O in Python.
|
| 3 |
+
See http://math.nist.gov/MatrixMarket/formats.html
|
| 4 |
+
for information about the Matrix Market format.
|
| 5 |
+
"""
|
| 6 |
+
#
|
| 7 |
+
# Author: Pearu Peterson <pearu@cens.ioc.ee>
|
| 8 |
+
# Created: October, 2004
|
| 9 |
+
#
|
| 10 |
+
# References:
|
| 11 |
+
# http://math.nist.gov/MatrixMarket/
|
| 12 |
+
#
|
| 13 |
+
import os
|
| 14 |
+
|
| 15 |
+
import numpy as np
|
| 16 |
+
from numpy import (asarray, real, imag, conj, zeros, ndarray, concatenate,
|
| 17 |
+
ones, can_cast)
|
| 18 |
+
|
| 19 |
+
from scipy.sparse import coo_matrix, issparse
|
| 20 |
+
|
| 21 |
+
__all__ = ['mminfo', 'mmread', 'mmwrite', 'MMFile']
|
| 22 |
+
|
| 23 |
+
|
| 24 |
+
# -----------------------------------------------------------------------------
|
| 25 |
+
def asstr(s):
|
| 26 |
+
if isinstance(s, bytes):
|
| 27 |
+
return s.decode('latin1')
|
| 28 |
+
return str(s)
|
| 29 |
+
|
| 30 |
+
|
| 31 |
+
def mminfo(source):
|
| 32 |
+
"""
|
| 33 |
+
Return size and storage parameters from Matrix Market file-like 'source'.
|
| 34 |
+
|
| 35 |
+
Parameters
|
| 36 |
+
----------
|
| 37 |
+
source : str or file-like
|
| 38 |
+
Matrix Market filename (extension .mtx) or open file-like object
|
| 39 |
+
|
| 40 |
+
Returns
|
| 41 |
+
-------
|
| 42 |
+
rows : int
|
| 43 |
+
Number of matrix rows.
|
| 44 |
+
cols : int
|
| 45 |
+
Number of matrix columns.
|
| 46 |
+
entries : int
|
| 47 |
+
Number of non-zero entries of a sparse matrix
|
| 48 |
+
or rows*cols for a dense matrix.
|
| 49 |
+
format : str
|
| 50 |
+
Either 'coordinate' or 'array'.
|
| 51 |
+
field : str
|
| 52 |
+
Either 'real', 'complex', 'pattern', or 'integer'.
|
| 53 |
+
symmetry : str
|
| 54 |
+
Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
|
| 55 |
+
|
| 56 |
+
Examples
|
| 57 |
+
--------
|
| 58 |
+
>>> from io import StringIO
|
| 59 |
+
>>> from scipy.io import mminfo
|
| 60 |
+
|
| 61 |
+
>>> text = '''%%MatrixMarket matrix coordinate real general
|
| 62 |
+
... 5 5 7
|
| 63 |
+
... 2 3 1.0
|
| 64 |
+
... 3 4 2.0
|
| 65 |
+
... 3 5 3.0
|
| 66 |
+
... 4 1 4.0
|
| 67 |
+
... 4 2 5.0
|
| 68 |
+
... 4 3 6.0
|
| 69 |
+
... 4 4 7.0
|
| 70 |
+
... '''
|
| 71 |
+
|
| 72 |
+
|
| 73 |
+
``mminfo(source)`` returns the number of rows, number of columns,
|
| 74 |
+
format, field type and symmetry attribute of the source file.
|
| 75 |
+
|
| 76 |
+
>>> mminfo(StringIO(text))
|
| 77 |
+
(5, 5, 7, 'coordinate', 'real', 'general')
|
| 78 |
+
"""
|
| 79 |
+
return MMFile.info(source)
|
| 80 |
+
|
| 81 |
+
# -----------------------------------------------------------------------------
|
| 82 |
+
|
| 83 |
+
|
| 84 |
+
def mmread(source):
|
| 85 |
+
"""
|
| 86 |
+
Reads the contents of a Matrix Market file-like 'source' into a matrix.
|
| 87 |
+
|
| 88 |
+
Parameters
|
| 89 |
+
----------
|
| 90 |
+
source : str or file-like
|
| 91 |
+
Matrix Market filename (extensions .mtx, .mtz.gz)
|
| 92 |
+
or open file-like object.
|
| 93 |
+
|
| 94 |
+
Returns
|
| 95 |
+
-------
|
| 96 |
+
a : ndarray or coo_matrix
|
| 97 |
+
Dense or sparse matrix depending on the matrix format in the
|
| 98 |
+
Matrix Market file.
|
| 99 |
+
|
| 100 |
+
Examples
|
| 101 |
+
--------
|
| 102 |
+
>>> from io import StringIO
|
| 103 |
+
>>> from scipy.io import mmread
|
| 104 |
+
|
| 105 |
+
>>> text = '''%%MatrixMarket matrix coordinate real general
|
| 106 |
+
... 5 5 7
|
| 107 |
+
... 2 3 1.0
|
| 108 |
+
... 3 4 2.0
|
| 109 |
+
... 3 5 3.0
|
| 110 |
+
... 4 1 4.0
|
| 111 |
+
... 4 2 5.0
|
| 112 |
+
... 4 3 6.0
|
| 113 |
+
... 4 4 7.0
|
| 114 |
+
... '''
|
| 115 |
+
|
| 116 |
+
``mmread(source)`` returns the data as sparse matrix in COO format.
|
| 117 |
+
|
| 118 |
+
>>> m = mmread(StringIO(text))
|
| 119 |
+
>>> m
|
| 120 |
+
<5x5 sparse matrix of type '<class 'numpy.float64'>'
|
| 121 |
+
with 7 stored elements in COOrdinate format>
|
| 122 |
+
>>> m.A
|
| 123 |
+
array([[0., 0., 0., 0., 0.],
|
| 124 |
+
[0., 0., 1., 0., 0.],
|
| 125 |
+
[0., 0., 0., 2., 3.],
|
| 126 |
+
[4., 5., 6., 7., 0.],
|
| 127 |
+
[0., 0., 0., 0., 0.]])
|
| 128 |
+
"""
|
| 129 |
+
return MMFile().read(source)
|
| 130 |
+
|
| 131 |
+
# -----------------------------------------------------------------------------
|
| 132 |
+
|
| 133 |
+
|
| 134 |
+
def mmwrite(target, a, comment='', field=None, precision=None, symmetry=None):
|
| 135 |
+
r"""
|
| 136 |
+
Writes the sparse or dense array `a` to Matrix Market file-like `target`.
|
| 137 |
+
|
| 138 |
+
Parameters
|
| 139 |
+
----------
|
| 140 |
+
target : str or file-like
|
| 141 |
+
Matrix Market filename (extension .mtx) or open file-like object.
|
| 142 |
+
a : array like
|
| 143 |
+
Sparse or dense 2-D array.
|
| 144 |
+
comment : str, optional
|
| 145 |
+
Comments to be prepended to the Matrix Market file.
|
| 146 |
+
field : None or str, optional
|
| 147 |
+
Either 'real', 'complex', 'pattern', or 'integer'.
|
| 148 |
+
precision : None or int, optional
|
| 149 |
+
Number of digits to display for real or complex values.
|
| 150 |
+
symmetry : None or str, optional
|
| 151 |
+
Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
|
| 152 |
+
If symmetry is None the symmetry type of 'a' is determined by its
|
| 153 |
+
values.
|
| 154 |
+
|
| 155 |
+
Returns
|
| 156 |
+
-------
|
| 157 |
+
None
|
| 158 |
+
|
| 159 |
+
Examples
|
| 160 |
+
--------
|
| 161 |
+
>>> from io import BytesIO
|
| 162 |
+
>>> import numpy as np
|
| 163 |
+
>>> from scipy.sparse import coo_matrix
|
| 164 |
+
>>> from scipy.io import mmwrite
|
| 165 |
+
|
| 166 |
+
Write a small NumPy array to a matrix market file. The file will be
|
| 167 |
+
written in the ``'array'`` format.
|
| 168 |
+
|
| 169 |
+
>>> a = np.array([[1.0, 0, 0, 0], [0, 2.5, 0, 6.25]])
|
| 170 |
+
>>> target = BytesIO()
|
| 171 |
+
>>> mmwrite(target, a)
|
| 172 |
+
>>> print(target.getvalue().decode('latin1'))
|
| 173 |
+
%%MatrixMarket matrix array real general
|
| 174 |
+
%
|
| 175 |
+
2 4
|
| 176 |
+
1.0000000000000000e+00
|
| 177 |
+
0.0000000000000000e+00
|
| 178 |
+
0.0000000000000000e+00
|
| 179 |
+
2.5000000000000000e+00
|
| 180 |
+
0.0000000000000000e+00
|
| 181 |
+
0.0000000000000000e+00
|
| 182 |
+
0.0000000000000000e+00
|
| 183 |
+
6.2500000000000000e+00
|
| 184 |
+
|
| 185 |
+
Add a comment to the output file, and set the precision to 3.
|
| 186 |
+
|
| 187 |
+
>>> target = BytesIO()
|
| 188 |
+
>>> mmwrite(target, a, comment='\n Some test data.\n', precision=3)
|
| 189 |
+
>>> print(target.getvalue().decode('latin1'))
|
| 190 |
+
%%MatrixMarket matrix array real general
|
| 191 |
+
%
|
| 192 |
+
% Some test data.
|
| 193 |
+
%
|
| 194 |
+
2 4
|
| 195 |
+
1.000e+00
|
| 196 |
+
0.000e+00
|
| 197 |
+
0.000e+00
|
| 198 |
+
2.500e+00
|
| 199 |
+
0.000e+00
|
| 200 |
+
0.000e+00
|
| 201 |
+
0.000e+00
|
| 202 |
+
6.250e+00
|
| 203 |
+
|
| 204 |
+
Convert to a sparse matrix before calling ``mmwrite``. This will
|
| 205 |
+
result in the output format being ``'coordinate'`` rather than
|
| 206 |
+
``'array'``.
|
| 207 |
+
|
| 208 |
+
>>> target = BytesIO()
|
| 209 |
+
>>> mmwrite(target, coo_matrix(a), precision=3)
|
| 210 |
+
>>> print(target.getvalue().decode('latin1'))
|
| 211 |
+
%%MatrixMarket matrix coordinate real general
|
| 212 |
+
%
|
| 213 |
+
2 4 3
|
| 214 |
+
1 1 1.00e+00
|
| 215 |
+
2 2 2.50e+00
|
| 216 |
+
2 4 6.25e+00
|
| 217 |
+
|
| 218 |
+
Write a complex Hermitian array to a matrix market file. Note that
|
| 219 |
+
only six values are actually written to the file; the other values
|
| 220 |
+
are implied by the symmetry.
|
| 221 |
+
|
| 222 |
+
>>> z = np.array([[3, 1+2j, 4-3j], [1-2j, 1, -5j], [4+3j, 5j, 2.5]])
|
| 223 |
+
>>> z
|
| 224 |
+
array([[ 3. +0.j, 1. +2.j, 4. -3.j],
|
| 225 |
+
[ 1. -2.j, 1. +0.j, -0. -5.j],
|
| 226 |
+
[ 4. +3.j, 0. +5.j, 2.5+0.j]])
|
| 227 |
+
|
| 228 |
+
>>> target = BytesIO()
|
| 229 |
+
>>> mmwrite(target, z, precision=2)
|
| 230 |
+
>>> print(target.getvalue().decode('latin1'))
|
| 231 |
+
%%MatrixMarket matrix array complex hermitian
|
| 232 |
+
%
|
| 233 |
+
3 3
|
| 234 |
+
3.00e+00 0.00e+00
|
| 235 |
+
1.00e+00 -2.00e+00
|
| 236 |
+
4.00e+00 3.00e+00
|
| 237 |
+
1.00e+00 0.00e+00
|
| 238 |
+
0.00e+00 5.00e+00
|
| 239 |
+
2.50e+00 0.00e+00
|
| 240 |
+
|
| 241 |
+
"""
|
| 242 |
+
MMFile().write(target, a, comment, field, precision, symmetry)
|
| 243 |
+
|
| 244 |
+
|
| 245 |
+
###############################################################################
|
| 246 |
+
class MMFile:
|
| 247 |
+
__slots__ = ('_rows',
|
| 248 |
+
'_cols',
|
| 249 |
+
'_entries',
|
| 250 |
+
'_format',
|
| 251 |
+
'_field',
|
| 252 |
+
'_symmetry')
|
| 253 |
+
|
| 254 |
+
@property
|
| 255 |
+
def rows(self):
|
| 256 |
+
return self._rows
|
| 257 |
+
|
| 258 |
+
@property
|
| 259 |
+
def cols(self):
|
| 260 |
+
return self._cols
|
| 261 |
+
|
| 262 |
+
@property
|
| 263 |
+
def entries(self):
|
| 264 |
+
return self._entries
|
| 265 |
+
|
| 266 |
+
@property
|
| 267 |
+
def format(self):
|
| 268 |
+
return self._format
|
| 269 |
+
|
| 270 |
+
@property
|
| 271 |
+
def field(self):
|
| 272 |
+
return self._field
|
| 273 |
+
|
| 274 |
+
@property
|
| 275 |
+
def symmetry(self):
|
| 276 |
+
return self._symmetry
|
| 277 |
+
|
| 278 |
+
@property
|
| 279 |
+
def has_symmetry(self):
|
| 280 |
+
return self._symmetry in (self.SYMMETRY_SYMMETRIC,
|
| 281 |
+
self.SYMMETRY_SKEW_SYMMETRIC,
|
| 282 |
+
self.SYMMETRY_HERMITIAN)
|
| 283 |
+
|
| 284 |
+
# format values
|
| 285 |
+
FORMAT_COORDINATE = 'coordinate'
|
| 286 |
+
FORMAT_ARRAY = 'array'
|
| 287 |
+
FORMAT_VALUES = (FORMAT_COORDINATE, FORMAT_ARRAY)
|
| 288 |
+
|
| 289 |
+
@classmethod
|
| 290 |
+
def _validate_format(self, format):
|
| 291 |
+
if format not in self.FORMAT_VALUES:
|
| 292 |
+
msg = f'unknown format type {format}, must be one of {self.FORMAT_VALUES}'
|
| 293 |
+
raise ValueError(msg)
|
| 294 |
+
|
| 295 |
+
# field values
|
| 296 |
+
FIELD_INTEGER = 'integer'
|
| 297 |
+
FIELD_UNSIGNED = 'unsigned-integer'
|
| 298 |
+
FIELD_REAL = 'real'
|
| 299 |
+
FIELD_COMPLEX = 'complex'
|
| 300 |
+
FIELD_PATTERN = 'pattern'
|
| 301 |
+
FIELD_VALUES = (FIELD_INTEGER, FIELD_UNSIGNED, FIELD_REAL, FIELD_COMPLEX,
|
| 302 |
+
FIELD_PATTERN)
|
| 303 |
+
|
| 304 |
+
@classmethod
|
| 305 |
+
def _validate_field(self, field):
|
| 306 |
+
if field not in self.FIELD_VALUES:
|
| 307 |
+
msg = f'unknown field type {field}, must be one of {self.FIELD_VALUES}'
|
| 308 |
+
raise ValueError(msg)
|
| 309 |
+
|
| 310 |
+
# symmetry values
|
| 311 |
+
SYMMETRY_GENERAL = 'general'
|
| 312 |
+
SYMMETRY_SYMMETRIC = 'symmetric'
|
| 313 |
+
SYMMETRY_SKEW_SYMMETRIC = 'skew-symmetric'
|
| 314 |
+
SYMMETRY_HERMITIAN = 'hermitian'
|
| 315 |
+
SYMMETRY_VALUES = (SYMMETRY_GENERAL, SYMMETRY_SYMMETRIC,
|
| 316 |
+
SYMMETRY_SKEW_SYMMETRIC, SYMMETRY_HERMITIAN)
|
| 317 |
+
|
| 318 |
+
@classmethod
|
| 319 |
+
def _validate_symmetry(self, symmetry):
|
| 320 |
+
if symmetry not in self.SYMMETRY_VALUES:
|
| 321 |
+
raise ValueError(f'unknown symmetry type {symmetry}, '
|
| 322 |
+
f'must be one of {self.SYMMETRY_VALUES}')
|
| 323 |
+
|
| 324 |
+
DTYPES_BY_FIELD = {FIELD_INTEGER: 'intp',
|
| 325 |
+
FIELD_UNSIGNED: 'uint64',
|
| 326 |
+
FIELD_REAL: 'd',
|
| 327 |
+
FIELD_COMPLEX: 'D',
|
| 328 |
+
FIELD_PATTERN: 'd'}
|
| 329 |
+
|
| 330 |
+
# -------------------------------------------------------------------------
|
| 331 |
+
@staticmethod
|
| 332 |
+
def reader():
|
| 333 |
+
pass
|
| 334 |
+
|
| 335 |
+
# -------------------------------------------------------------------------
|
| 336 |
+
@staticmethod
|
| 337 |
+
def writer():
|
| 338 |
+
pass
|
| 339 |
+
|
| 340 |
+
# -------------------------------------------------------------------------
|
| 341 |
+
@classmethod
|
| 342 |
+
def info(self, source):
|
| 343 |
+
"""
|
| 344 |
+
Return size, storage parameters from Matrix Market file-like 'source'.
|
| 345 |
+
|
| 346 |
+
Parameters
|
| 347 |
+
----------
|
| 348 |
+
source : str or file-like
|
| 349 |
+
Matrix Market filename (extension .mtx) or open file-like object
|
| 350 |
+
|
| 351 |
+
Returns
|
| 352 |
+
-------
|
| 353 |
+
rows : int
|
| 354 |
+
Number of matrix rows.
|
| 355 |
+
cols : int
|
| 356 |
+
Number of matrix columns.
|
| 357 |
+
entries : int
|
| 358 |
+
Number of non-zero entries of a sparse matrix
|
| 359 |
+
or rows*cols for a dense matrix.
|
| 360 |
+
format : str
|
| 361 |
+
Either 'coordinate' or 'array'.
|
| 362 |
+
field : str
|
| 363 |
+
Either 'real', 'complex', 'pattern', or 'integer'.
|
| 364 |
+
symmetry : str
|
| 365 |
+
Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
|
| 366 |
+
"""
|
| 367 |
+
|
| 368 |
+
stream, close_it = self._open(source)
|
| 369 |
+
|
| 370 |
+
try:
|
| 371 |
+
|
| 372 |
+
# read and validate header line
|
| 373 |
+
line = stream.readline()
|
| 374 |
+
mmid, matrix, format, field, symmetry = \
|
| 375 |
+
(asstr(part.strip()) for part in line.split())
|
| 376 |
+
if not mmid.startswith('%%MatrixMarket'):
|
| 377 |
+
raise ValueError('source is not in Matrix Market format')
|
| 378 |
+
if not matrix.lower() == 'matrix':
|
| 379 |
+
raise ValueError("Problem reading file header: " + line)
|
| 380 |
+
|
| 381 |
+
# http://math.nist.gov/MatrixMarket/formats.html
|
| 382 |
+
if format.lower() == 'array':
|
| 383 |
+
format = self.FORMAT_ARRAY
|
| 384 |
+
elif format.lower() == 'coordinate':
|
| 385 |
+
format = self.FORMAT_COORDINATE
|
| 386 |
+
|
| 387 |
+
# skip comments
|
| 388 |
+
# line.startswith('%')
|
| 389 |
+
while line:
|
| 390 |
+
if line.lstrip() and line.lstrip()[0] in ['%', 37]:
|
| 391 |
+
line = stream.readline()
|
| 392 |
+
else:
|
| 393 |
+
break
|
| 394 |
+
|
| 395 |
+
# skip empty lines
|
| 396 |
+
while not line.strip():
|
| 397 |
+
line = stream.readline()
|
| 398 |
+
|
| 399 |
+
split_line = line.split()
|
| 400 |
+
if format == self.FORMAT_ARRAY:
|
| 401 |
+
if not len(split_line) == 2:
|
| 402 |
+
raise ValueError("Header line not of length 2: " +
|
| 403 |
+
line.decode('ascii'))
|
| 404 |
+
rows, cols = map(int, split_line)
|
| 405 |
+
entries = rows * cols
|
| 406 |
+
else:
|
| 407 |
+
if not len(split_line) == 3:
|
| 408 |
+
raise ValueError("Header line not of length 3: " +
|
| 409 |
+
line.decode('ascii'))
|
| 410 |
+
rows, cols, entries = map(int, split_line)
|
| 411 |
+
|
| 412 |
+
return (rows, cols, entries, format, field.lower(),
|
| 413 |
+
symmetry.lower())
|
| 414 |
+
|
| 415 |
+
finally:
|
| 416 |
+
if close_it:
|
| 417 |
+
stream.close()
|
| 418 |
+
|
| 419 |
+
# -------------------------------------------------------------------------
|
| 420 |
+
@staticmethod
|
| 421 |
+
def _open(filespec, mode='rb'):
|
| 422 |
+
""" Return an open file stream for reading based on source.
|
| 423 |
+
|
| 424 |
+
If source is a file name, open it (after trying to find it with mtx and
|
| 425 |
+
gzipped mtx extensions). Otherwise, just return source.
|
| 426 |
+
|
| 427 |
+
Parameters
|
| 428 |
+
----------
|
| 429 |
+
filespec : str or file-like
|
| 430 |
+
String giving file name or file-like object
|
| 431 |
+
mode : str, optional
|
| 432 |
+
Mode with which to open file, if `filespec` is a file name.
|
| 433 |
+
|
| 434 |
+
Returns
|
| 435 |
+
-------
|
| 436 |
+
fobj : file-like
|
| 437 |
+
Open file-like object.
|
| 438 |
+
close_it : bool
|
| 439 |
+
True if the calling function should close this file when done,
|
| 440 |
+
false otherwise.
|
| 441 |
+
"""
|
| 442 |
+
# If 'filespec' is path-like (str, pathlib.Path, os.DirEntry, other class
|
| 443 |
+
# implementing a '__fspath__' method), try to convert it to str. If this
|
| 444 |
+
# fails by throwing a 'TypeError', assume it's an open file handle and
|
| 445 |
+
# return it as-is.
|
| 446 |
+
try:
|
| 447 |
+
filespec = os.fspath(filespec)
|
| 448 |
+
except TypeError:
|
| 449 |
+
return filespec, False
|
| 450 |
+
|
| 451 |
+
# 'filespec' is definitely a str now
|
| 452 |
+
|
| 453 |
+
# open for reading
|
| 454 |
+
if mode[0] == 'r':
|
| 455 |
+
|
| 456 |
+
# determine filename plus extension
|
| 457 |
+
if not os.path.isfile(filespec):
|
| 458 |
+
if os.path.isfile(filespec+'.mtx'):
|
| 459 |
+
filespec = filespec + '.mtx'
|
| 460 |
+
elif os.path.isfile(filespec+'.mtx.gz'):
|
| 461 |
+
filespec = filespec + '.mtx.gz'
|
| 462 |
+
elif os.path.isfile(filespec+'.mtx.bz2'):
|
| 463 |
+
filespec = filespec + '.mtx.bz2'
|
| 464 |
+
# open filename
|
| 465 |
+
if filespec.endswith('.gz'):
|
| 466 |
+
import gzip
|
| 467 |
+
stream = gzip.open(filespec, mode)
|
| 468 |
+
elif filespec.endswith('.bz2'):
|
| 469 |
+
import bz2
|
| 470 |
+
stream = bz2.BZ2File(filespec, 'rb')
|
| 471 |
+
else:
|
| 472 |
+
stream = open(filespec, mode)
|
| 473 |
+
|
| 474 |
+
# open for writing
|
| 475 |
+
else:
|
| 476 |
+
if filespec[-4:] != '.mtx':
|
| 477 |
+
filespec = filespec + '.mtx'
|
| 478 |
+
stream = open(filespec, mode)
|
| 479 |
+
|
| 480 |
+
return stream, True
|
| 481 |
+
|
| 482 |
+
# -------------------------------------------------------------------------
|
| 483 |
+
@staticmethod
|
| 484 |
+
def _get_symmetry(a):
|
| 485 |
+
m, n = a.shape
|
| 486 |
+
if m != n:
|
| 487 |
+
return MMFile.SYMMETRY_GENERAL
|
| 488 |
+
issymm = True
|
| 489 |
+
isskew = True
|
| 490 |
+
isherm = a.dtype.char in 'FD'
|
| 491 |
+
|
| 492 |
+
# sparse input
|
| 493 |
+
if issparse(a):
|
| 494 |
+
# check if number of nonzero entries of lower and upper triangle
|
| 495 |
+
# matrix are equal
|
| 496 |
+
a = a.tocoo()
|
| 497 |
+
(row, col) = a.nonzero()
|
| 498 |
+
if (row < col).sum() != (row > col).sum():
|
| 499 |
+
return MMFile.SYMMETRY_GENERAL
|
| 500 |
+
|
| 501 |
+
# define iterator over symmetric pair entries
|
| 502 |
+
a = a.todok()
|
| 503 |
+
|
| 504 |
+
def symm_iterator():
|
| 505 |
+
for ((i, j), aij) in a.items():
|
| 506 |
+
if i > j:
|
| 507 |
+
aji = a[j, i]
|
| 508 |
+
yield (aij, aji, False)
|
| 509 |
+
elif i == j:
|
| 510 |
+
yield (aij, aij, True)
|
| 511 |
+
|
| 512 |
+
# non-sparse input
|
| 513 |
+
else:
|
| 514 |
+
# define iterator over symmetric pair entries
|
| 515 |
+
def symm_iterator():
|
| 516 |
+
for j in range(n):
|
| 517 |
+
for i in range(j, n):
|
| 518 |
+
aij, aji = a[i][j], a[j][i]
|
| 519 |
+
yield (aij, aji, i == j)
|
| 520 |
+
|
| 521 |
+
# check for symmetry
|
| 522 |
+
# yields aij, aji, is_diagonal
|
| 523 |
+
for (aij, aji, is_diagonal) in symm_iterator():
|
| 524 |
+
if isskew and is_diagonal and aij != 0:
|
| 525 |
+
isskew = False
|
| 526 |
+
else:
|
| 527 |
+
if issymm and aij != aji:
|
| 528 |
+
issymm = False
|
| 529 |
+
with np.errstate(over="ignore"):
|
| 530 |
+
# This can give a warning for uint dtypes, so silence that
|
| 531 |
+
if isskew and aij != -aji:
|
| 532 |
+
isskew = False
|
| 533 |
+
if isherm and aij != conj(aji):
|
| 534 |
+
isherm = False
|
| 535 |
+
if not (issymm or isskew or isherm):
|
| 536 |
+
break
|
| 537 |
+
|
| 538 |
+
# return symmetry value
|
| 539 |
+
if issymm:
|
| 540 |
+
return MMFile.SYMMETRY_SYMMETRIC
|
| 541 |
+
if isskew:
|
| 542 |
+
return MMFile.SYMMETRY_SKEW_SYMMETRIC
|
| 543 |
+
if isherm:
|
| 544 |
+
return MMFile.SYMMETRY_HERMITIAN
|
| 545 |
+
return MMFile.SYMMETRY_GENERAL
|
| 546 |
+
|
| 547 |
+
# -------------------------------------------------------------------------
|
| 548 |
+
@staticmethod
|
| 549 |
+
def _field_template(field, precision):
|
| 550 |
+
return {MMFile.FIELD_REAL: '%%.%ie\n' % precision,
|
| 551 |
+
MMFile.FIELD_INTEGER: '%i\n',
|
| 552 |
+
MMFile.FIELD_UNSIGNED: '%u\n',
|
| 553 |
+
MMFile.FIELD_COMPLEX: '%%.%ie %%.%ie\n' %
|
| 554 |
+
(precision, precision)
|
| 555 |
+
}.get(field, None)
|
| 556 |
+
|
| 557 |
+
# -------------------------------------------------------------------------
|
| 558 |
+
def __init__(self, **kwargs):
|
| 559 |
+
self._init_attrs(**kwargs)
|
| 560 |
+
|
| 561 |
+
# -------------------------------------------------------------------------
|
| 562 |
+
def read(self, source):
|
| 563 |
+
"""
|
| 564 |
+
Reads the contents of a Matrix Market file-like 'source' into a matrix.
|
| 565 |
+
|
| 566 |
+
Parameters
|
| 567 |
+
----------
|
| 568 |
+
source : str or file-like
|
| 569 |
+
Matrix Market filename (extensions .mtx, .mtz.gz)
|
| 570 |
+
or open file object.
|
| 571 |
+
|
| 572 |
+
Returns
|
| 573 |
+
-------
|
| 574 |
+
a : ndarray or coo_matrix
|
| 575 |
+
Dense or sparse matrix depending on the matrix format in the
|
| 576 |
+
Matrix Market file.
|
| 577 |
+
"""
|
| 578 |
+
stream, close_it = self._open(source)
|
| 579 |
+
|
| 580 |
+
try:
|
| 581 |
+
self._parse_header(stream)
|
| 582 |
+
return self._parse_body(stream)
|
| 583 |
+
|
| 584 |
+
finally:
|
| 585 |
+
if close_it:
|
| 586 |
+
stream.close()
|
| 587 |
+
|
| 588 |
+
# -------------------------------------------------------------------------
|
| 589 |
+
def write(self, target, a, comment='', field=None, precision=None,
|
| 590 |
+
symmetry=None):
|
| 591 |
+
"""
|
| 592 |
+
Writes sparse or dense array `a` to Matrix Market file-like `target`.
|
| 593 |
+
|
| 594 |
+
Parameters
|
| 595 |
+
----------
|
| 596 |
+
target : str or file-like
|
| 597 |
+
Matrix Market filename (extension .mtx) or open file-like object.
|
| 598 |
+
a : array like
|
| 599 |
+
Sparse or dense 2-D array.
|
| 600 |
+
comment : str, optional
|
| 601 |
+
Comments to be prepended to the Matrix Market file.
|
| 602 |
+
field : None or str, optional
|
| 603 |
+
Either 'real', 'complex', 'pattern', or 'integer'.
|
| 604 |
+
precision : None or int, optional
|
| 605 |
+
Number of digits to display for real or complex values.
|
| 606 |
+
symmetry : None or str, optional
|
| 607 |
+
Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
|
| 608 |
+
If symmetry is None the symmetry type of 'a' is determined by its
|
| 609 |
+
values.
|
| 610 |
+
"""
|
| 611 |
+
|
| 612 |
+
stream, close_it = self._open(target, 'wb')
|
| 613 |
+
|
| 614 |
+
try:
|
| 615 |
+
self._write(stream, a, comment, field, precision, symmetry)
|
| 616 |
+
|
| 617 |
+
finally:
|
| 618 |
+
if close_it:
|
| 619 |
+
stream.close()
|
| 620 |
+
else:
|
| 621 |
+
stream.flush()
|
| 622 |
+
|
| 623 |
+
# -------------------------------------------------------------------------
|
| 624 |
+
def _init_attrs(self, **kwargs):
|
| 625 |
+
"""
|
| 626 |
+
Initialize each attributes with the corresponding keyword arg value
|
| 627 |
+
or a default of None
|
| 628 |
+
"""
|
| 629 |
+
|
| 630 |
+
attrs = self.__class__.__slots__
|
| 631 |
+
public_attrs = [attr[1:] for attr in attrs]
|
| 632 |
+
invalid_keys = set(kwargs.keys()) - set(public_attrs)
|
| 633 |
+
|
| 634 |
+
if invalid_keys:
|
| 635 |
+
raise ValueError('''found {} invalid keyword arguments, please only
|
| 636 |
+
use {}'''.format(tuple(invalid_keys),
|
| 637 |
+
public_attrs))
|
| 638 |
+
|
| 639 |
+
for attr in attrs:
|
| 640 |
+
setattr(self, attr, kwargs.get(attr[1:], None))
|
| 641 |
+
|
| 642 |
+
# -------------------------------------------------------------------------
|
| 643 |
+
def _parse_header(self, stream):
|
| 644 |
+
rows, cols, entries, format, field, symmetry = \
|
| 645 |
+
self.__class__.info(stream)
|
| 646 |
+
self._init_attrs(rows=rows, cols=cols, entries=entries, format=format,
|
| 647 |
+
field=field, symmetry=symmetry)
|
| 648 |
+
|
| 649 |
+
# -------------------------------------------------------------------------
|
| 650 |
+
def _parse_body(self, stream):
|
| 651 |
+
rows, cols, entries, format, field, symm = (self.rows, self.cols,
|
| 652 |
+
self.entries, self.format,
|
| 653 |
+
self.field, self.symmetry)
|
| 654 |
+
|
| 655 |
+
dtype = self.DTYPES_BY_FIELD.get(field, None)
|
| 656 |
+
|
| 657 |
+
has_symmetry = self.has_symmetry
|
| 658 |
+
is_integer = field == self.FIELD_INTEGER
|
| 659 |
+
is_unsigned_integer = field == self.FIELD_UNSIGNED
|
| 660 |
+
is_complex = field == self.FIELD_COMPLEX
|
| 661 |
+
is_skew = symm == self.SYMMETRY_SKEW_SYMMETRIC
|
| 662 |
+
is_herm = symm == self.SYMMETRY_HERMITIAN
|
| 663 |
+
is_pattern = field == self.FIELD_PATTERN
|
| 664 |
+
|
| 665 |
+
if format == self.FORMAT_ARRAY:
|
| 666 |
+
a = zeros((rows, cols), dtype=dtype)
|
| 667 |
+
line = 1
|
| 668 |
+
i, j = 0, 0
|
| 669 |
+
if is_skew:
|
| 670 |
+
a[i, j] = 0
|
| 671 |
+
if i < rows - 1:
|
| 672 |
+
i += 1
|
| 673 |
+
while line:
|
| 674 |
+
line = stream.readline()
|
| 675 |
+
# line.startswith('%')
|
| 676 |
+
if not line or line[0] in ['%', 37] or not line.strip():
|
| 677 |
+
continue
|
| 678 |
+
if is_integer:
|
| 679 |
+
aij = int(line)
|
| 680 |
+
elif is_unsigned_integer:
|
| 681 |
+
aij = int(line)
|
| 682 |
+
elif is_complex:
|
| 683 |
+
aij = complex(*map(float, line.split()))
|
| 684 |
+
else:
|
| 685 |
+
aij = float(line)
|
| 686 |
+
a[i, j] = aij
|
| 687 |
+
if has_symmetry and i != j:
|
| 688 |
+
if is_skew:
|
| 689 |
+
a[j, i] = -aij
|
| 690 |
+
elif is_herm:
|
| 691 |
+
a[j, i] = conj(aij)
|
| 692 |
+
else:
|
| 693 |
+
a[j, i] = aij
|
| 694 |
+
if i < rows-1:
|
| 695 |
+
i = i + 1
|
| 696 |
+
else:
|
| 697 |
+
j = j + 1
|
| 698 |
+
if not has_symmetry:
|
| 699 |
+
i = 0
|
| 700 |
+
else:
|
| 701 |
+
i = j
|
| 702 |
+
if is_skew:
|
| 703 |
+
a[i, j] = 0
|
| 704 |
+
if i < rows-1:
|
| 705 |
+
i += 1
|
| 706 |
+
|
| 707 |
+
if is_skew:
|
| 708 |
+
if not (i in [0, j] and j == cols - 1):
|
| 709 |
+
raise ValueError("Parse error, did not read all lines.")
|
| 710 |
+
else:
|
| 711 |
+
if not (i in [0, j] and j == cols):
|
| 712 |
+
raise ValueError("Parse error, did not read all lines.")
|
| 713 |
+
|
| 714 |
+
elif format == self.FORMAT_COORDINATE:
|
| 715 |
+
# Read sparse COOrdinate format
|
| 716 |
+
|
| 717 |
+
if entries == 0:
|
| 718 |
+
# empty matrix
|
| 719 |
+
return coo_matrix((rows, cols), dtype=dtype)
|
| 720 |
+
|
| 721 |
+
I = zeros(entries, dtype='intc')
|
| 722 |
+
J = zeros(entries, dtype='intc')
|
| 723 |
+
if is_pattern:
|
| 724 |
+
V = ones(entries, dtype='int8')
|
| 725 |
+
elif is_integer:
|
| 726 |
+
V = zeros(entries, dtype='intp')
|
| 727 |
+
elif is_unsigned_integer:
|
| 728 |
+
V = zeros(entries, dtype='uint64')
|
| 729 |
+
elif is_complex:
|
| 730 |
+
V = zeros(entries, dtype='complex')
|
| 731 |
+
else:
|
| 732 |
+
V = zeros(entries, dtype='float')
|
| 733 |
+
|
| 734 |
+
entry_number = 0
|
| 735 |
+
for line in stream:
|
| 736 |
+
# line.startswith('%')
|
| 737 |
+
if not line or line[0] in ['%', 37] or not line.strip():
|
| 738 |
+
continue
|
| 739 |
+
|
| 740 |
+
if entry_number+1 > entries:
|
| 741 |
+
raise ValueError("'entries' in header is smaller than "
|
| 742 |
+
"number of entries")
|
| 743 |
+
l = line.split()
|
| 744 |
+
I[entry_number], J[entry_number] = map(int, l[:2])
|
| 745 |
+
|
| 746 |
+
if not is_pattern:
|
| 747 |
+
if is_integer:
|
| 748 |
+
V[entry_number] = int(l[2])
|
| 749 |
+
elif is_unsigned_integer:
|
| 750 |
+
V[entry_number] = int(l[2])
|
| 751 |
+
elif is_complex:
|
| 752 |
+
V[entry_number] = complex(*map(float, l[2:]))
|
| 753 |
+
else:
|
| 754 |
+
V[entry_number] = float(l[2])
|
| 755 |
+
entry_number += 1
|
| 756 |
+
if entry_number < entries:
|
| 757 |
+
raise ValueError("'entries' in header is larger than "
|
| 758 |
+
"number of entries")
|
| 759 |
+
|
| 760 |
+
I -= 1 # adjust indices (base 1 -> base 0)
|
| 761 |
+
J -= 1
|
| 762 |
+
|
| 763 |
+
if has_symmetry:
|
| 764 |
+
mask = (I != J) # off diagonal mask
|
| 765 |
+
od_I = I[mask]
|
| 766 |
+
od_J = J[mask]
|
| 767 |
+
od_V = V[mask]
|
| 768 |
+
|
| 769 |
+
I = concatenate((I, od_J))
|
| 770 |
+
J = concatenate((J, od_I))
|
| 771 |
+
|
| 772 |
+
if is_skew:
|
| 773 |
+
od_V *= -1
|
| 774 |
+
elif is_herm:
|
| 775 |
+
od_V = od_V.conjugate()
|
| 776 |
+
|
| 777 |
+
V = concatenate((V, od_V))
|
| 778 |
+
|
| 779 |
+
a = coo_matrix((V, (I, J)), shape=(rows, cols), dtype=dtype)
|
| 780 |
+
else:
|
| 781 |
+
raise NotImplementedError(format)
|
| 782 |
+
|
| 783 |
+
return a
|
| 784 |
+
|
| 785 |
+
# ------------------------------------------------------------------------
|
| 786 |
+
def _write(self, stream, a, comment='', field=None, precision=None,
|
| 787 |
+
symmetry=None):
|
| 788 |
+
if isinstance(a, list) or isinstance(a, ndarray) or \
|
| 789 |
+
isinstance(a, tuple) or hasattr(a, '__array__'):
|
| 790 |
+
rep = self.FORMAT_ARRAY
|
| 791 |
+
a = asarray(a)
|
| 792 |
+
if len(a.shape) != 2:
|
| 793 |
+
raise ValueError('Expected 2 dimensional array')
|
| 794 |
+
rows, cols = a.shape
|
| 795 |
+
|
| 796 |
+
if field is not None:
|
| 797 |
+
|
| 798 |
+
if field == self.FIELD_INTEGER:
|
| 799 |
+
if not can_cast(a.dtype, 'intp'):
|
| 800 |
+
raise OverflowError("mmwrite does not support integer "
|
| 801 |
+
"dtypes larger than native 'intp'.")
|
| 802 |
+
a = a.astype('intp')
|
| 803 |
+
elif field == self.FIELD_REAL:
|
| 804 |
+
if a.dtype.char not in 'fd':
|
| 805 |
+
a = a.astype('d')
|
| 806 |
+
elif field == self.FIELD_COMPLEX:
|
| 807 |
+
if a.dtype.char not in 'FD':
|
| 808 |
+
a = a.astype('D')
|
| 809 |
+
|
| 810 |
+
else:
|
| 811 |
+
if not issparse(a):
|
| 812 |
+
raise ValueError('unknown matrix type: %s' % type(a))
|
| 813 |
+
|
| 814 |
+
rep = 'coordinate'
|
| 815 |
+
rows, cols = a.shape
|
| 816 |
+
|
| 817 |
+
typecode = a.dtype.char
|
| 818 |
+
|
| 819 |
+
if precision is None:
|
| 820 |
+
if typecode in 'fF':
|
| 821 |
+
precision = 8
|
| 822 |
+
else:
|
| 823 |
+
precision = 16
|
| 824 |
+
if field is None:
|
| 825 |
+
kind = a.dtype.kind
|
| 826 |
+
if kind == 'i':
|
| 827 |
+
if not can_cast(a.dtype, 'intp'):
|
| 828 |
+
raise OverflowError("mmwrite does not support integer "
|
| 829 |
+
"dtypes larger than native 'intp'.")
|
| 830 |
+
field = 'integer'
|
| 831 |
+
elif kind == 'f':
|
| 832 |
+
field = 'real'
|
| 833 |
+
elif kind == 'c':
|
| 834 |
+
field = 'complex'
|
| 835 |
+
elif kind == 'u':
|
| 836 |
+
field = 'unsigned-integer'
|
| 837 |
+
else:
|
| 838 |
+
raise TypeError('unexpected dtype kind ' + kind)
|
| 839 |
+
|
| 840 |
+
if symmetry is None:
|
| 841 |
+
symmetry = self._get_symmetry(a)
|
| 842 |
+
|
| 843 |
+
# validate rep, field, and symmetry
|
| 844 |
+
self.__class__._validate_format(rep)
|
| 845 |
+
self.__class__._validate_field(field)
|
| 846 |
+
self.__class__._validate_symmetry(symmetry)
|
| 847 |
+
|
| 848 |
+
# write initial header line
|
| 849 |
+
data = f'%%MatrixMarket matrix {rep} {field} {symmetry}\n'
|
| 850 |
+
stream.write(data.encode('latin1'))
|
| 851 |
+
|
| 852 |
+
# write comments
|
| 853 |
+
for line in comment.split('\n'):
|
| 854 |
+
data = '%%%s\n' % (line)
|
| 855 |
+
stream.write(data.encode('latin1'))
|
| 856 |
+
|
| 857 |
+
template = self._field_template(field, precision)
|
| 858 |
+
# write dense format
|
| 859 |
+
if rep == self.FORMAT_ARRAY:
|
| 860 |
+
# write shape spec
|
| 861 |
+
data = '%i %i\n' % (rows, cols)
|
| 862 |
+
stream.write(data.encode('latin1'))
|
| 863 |
+
|
| 864 |
+
if field in (self.FIELD_INTEGER, self.FIELD_REAL,
|
| 865 |
+
self.FIELD_UNSIGNED):
|
| 866 |
+
if symmetry == self.SYMMETRY_GENERAL:
|
| 867 |
+
for j in range(cols):
|
| 868 |
+
for i in range(rows):
|
| 869 |
+
data = template % a[i, j]
|
| 870 |
+
stream.write(data.encode('latin1'))
|
| 871 |
+
|
| 872 |
+
elif symmetry == self.SYMMETRY_SKEW_SYMMETRIC:
|
| 873 |
+
for j in range(cols):
|
| 874 |
+
for i in range(j + 1, rows):
|
| 875 |
+
data = template % a[i, j]
|
| 876 |
+
stream.write(data.encode('latin1'))
|
| 877 |
+
|
| 878 |
+
else:
|
| 879 |
+
for j in range(cols):
|
| 880 |
+
for i in range(j, rows):
|
| 881 |
+
data = template % a[i, j]
|
| 882 |
+
stream.write(data.encode('latin1'))
|
| 883 |
+
|
| 884 |
+
elif field == self.FIELD_COMPLEX:
|
| 885 |
+
|
| 886 |
+
if symmetry == self.SYMMETRY_GENERAL:
|
| 887 |
+
for j in range(cols):
|
| 888 |
+
for i in range(rows):
|
| 889 |
+
aij = a[i, j]
|
| 890 |
+
data = template % (real(aij), imag(aij))
|
| 891 |
+
stream.write(data.encode('latin1'))
|
| 892 |
+
else:
|
| 893 |
+
for j in range(cols):
|
| 894 |
+
for i in range(j, rows):
|
| 895 |
+
aij = a[i, j]
|
| 896 |
+
data = template % (real(aij), imag(aij))
|
| 897 |
+
stream.write(data.encode('latin1'))
|
| 898 |
+
|
| 899 |
+
elif field == self.FIELD_PATTERN:
|
| 900 |
+
raise ValueError('pattern type inconsisted with dense format')
|
| 901 |
+
|
| 902 |
+
else:
|
| 903 |
+
raise TypeError('Unknown field type %s' % field)
|
| 904 |
+
|
| 905 |
+
# write sparse format
|
| 906 |
+
else:
|
| 907 |
+
coo = a.tocoo() # convert to COOrdinate format
|
| 908 |
+
|
| 909 |
+
# if symmetry format used, remove values above main diagonal
|
| 910 |
+
if symmetry != self.SYMMETRY_GENERAL:
|
| 911 |
+
lower_triangle_mask = coo.row >= coo.col
|
| 912 |
+
coo = coo_matrix((coo.data[lower_triangle_mask],
|
| 913 |
+
(coo.row[lower_triangle_mask],
|
| 914 |
+
coo.col[lower_triangle_mask])),
|
| 915 |
+
shape=coo.shape)
|
| 916 |
+
|
| 917 |
+
# write shape spec
|
| 918 |
+
data = '%i %i %i\n' % (rows, cols, coo.nnz)
|
| 919 |
+
stream.write(data.encode('latin1'))
|
| 920 |
+
|
| 921 |
+
template = self._field_template(field, precision-1)
|
| 922 |
+
|
| 923 |
+
if field == self.FIELD_PATTERN:
|
| 924 |
+
for r, c in zip(coo.row+1, coo.col+1):
|
| 925 |
+
data = "%i %i\n" % (r, c)
|
| 926 |
+
stream.write(data.encode('latin1'))
|
| 927 |
+
elif field in (self.FIELD_INTEGER, self.FIELD_REAL,
|
| 928 |
+
self.FIELD_UNSIGNED):
|
| 929 |
+
for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
|
| 930 |
+
data = ("%i %i " % (r, c)) + (template % d)
|
| 931 |
+
stream.write(data.encode('latin1'))
|
| 932 |
+
elif field == self.FIELD_COMPLEX:
|
| 933 |
+
for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
|
| 934 |
+
data = ("%i %i " % (r, c)) + (template % (d.real, d.imag))
|
| 935 |
+
stream.write(data.encode('latin1'))
|
| 936 |
+
else:
|
| 937 |
+
raise TypeError('Unknown field type %s' % field)
|
| 938 |
+
|
| 939 |
+
|
| 940 |
+
def _is_fromfile_compatible(stream):
|
| 941 |
+
"""
|
| 942 |
+
Check whether `stream` is compatible with numpy.fromfile.
|
| 943 |
+
|
| 944 |
+
Passing a gzipped file object to ``fromfile/fromstring`` doesn't work with
|
| 945 |
+
Python 3.
|
| 946 |
+
"""
|
| 947 |
+
|
| 948 |
+
bad_cls = []
|
| 949 |
+
try:
|
| 950 |
+
import gzip
|
| 951 |
+
bad_cls.append(gzip.GzipFile)
|
| 952 |
+
except ImportError:
|
| 953 |
+
pass
|
| 954 |
+
try:
|
| 955 |
+
import bz2
|
| 956 |
+
bad_cls.append(bz2.BZ2File)
|
| 957 |
+
except ImportError:
|
| 958 |
+
pass
|
| 959 |
+
|
| 960 |
+
bad_cls = tuple(bad_cls)
|
| 961 |
+
return not isinstance(stream, bad_cls)
|
videochat2/lib/python3.10/site-packages/scipy/io/_netcdf.py
ADDED
|
@@ -0,0 +1,1095 @@
|
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|
| 1 |
+
"""
|
| 2 |
+
NetCDF reader/writer module.
|
| 3 |
+
|
| 4 |
+
This module is used to read and create NetCDF files. NetCDF files are
|
| 5 |
+
accessed through the `netcdf_file` object. Data written to and from NetCDF
|
| 6 |
+
files are contained in `netcdf_variable` objects. Attributes are given
|
| 7 |
+
as member variables of the `netcdf_file` and `netcdf_variable` objects.
|
| 8 |
+
|
| 9 |
+
This module implements the Scientific.IO.NetCDF API to read and create
|
| 10 |
+
NetCDF files. The same API is also used in the PyNIO and pynetcdf
|
| 11 |
+
modules, allowing these modules to be used interchangeably when working
|
| 12 |
+
with NetCDF files.
|
| 13 |
+
|
| 14 |
+
Only NetCDF3 is supported here; for NetCDF4 see
|
| 15 |
+
`netCDF4-python <http://unidata.github.io/netcdf4-python/>`__,
|
| 16 |
+
which has a similar API.
|
| 17 |
+
|
| 18 |
+
"""
|
| 19 |
+
|
| 20 |
+
# TODO:
|
| 21 |
+
# * properly implement ``_FillValue``.
|
| 22 |
+
# * fix character variables.
|
| 23 |
+
# * implement PAGESIZE for Python 2.6?
|
| 24 |
+
|
| 25 |
+
# The Scientific.IO.NetCDF API allows attributes to be added directly to
|
| 26 |
+
# instances of ``netcdf_file`` and ``netcdf_variable``. To differentiate
|
| 27 |
+
# between user-set attributes and instance attributes, user-set attributes
|
| 28 |
+
# are automatically stored in the ``_attributes`` attribute by overloading
|
| 29 |
+
#``__setattr__``. This is the reason why the code sometimes uses
|
| 30 |
+
#``obj.__dict__['key'] = value``, instead of simply ``obj.key = value``;
|
| 31 |
+
# otherwise the key would be inserted into userspace attributes.
|
| 32 |
+
|
| 33 |
+
|
| 34 |
+
__all__ = ['netcdf_file', 'netcdf_variable']
|
| 35 |
+
|
| 36 |
+
|
| 37 |
+
import warnings
|
| 38 |
+
import weakref
|
| 39 |
+
from operator import mul
|
| 40 |
+
from platform import python_implementation
|
| 41 |
+
|
| 42 |
+
import mmap as mm
|
| 43 |
+
|
| 44 |
+
import numpy as np
|
| 45 |
+
from numpy import frombuffer, dtype, empty, array, asarray
|
| 46 |
+
from numpy import little_endian as LITTLE_ENDIAN
|
| 47 |
+
from functools import reduce
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
IS_PYPY = python_implementation() == 'PyPy'
|
| 51 |
+
|
| 52 |
+
ABSENT = b'\x00\x00\x00\x00\x00\x00\x00\x00'
|
| 53 |
+
ZERO = b'\x00\x00\x00\x00'
|
| 54 |
+
NC_BYTE = b'\x00\x00\x00\x01'
|
| 55 |
+
NC_CHAR = b'\x00\x00\x00\x02'
|
| 56 |
+
NC_SHORT = b'\x00\x00\x00\x03'
|
| 57 |
+
NC_INT = b'\x00\x00\x00\x04'
|
| 58 |
+
NC_FLOAT = b'\x00\x00\x00\x05'
|
| 59 |
+
NC_DOUBLE = b'\x00\x00\x00\x06'
|
| 60 |
+
NC_DIMENSION = b'\x00\x00\x00\n'
|
| 61 |
+
NC_VARIABLE = b'\x00\x00\x00\x0b'
|
| 62 |
+
NC_ATTRIBUTE = b'\x00\x00\x00\x0c'
|
| 63 |
+
FILL_BYTE = b'\x81'
|
| 64 |
+
FILL_CHAR = b'\x00'
|
| 65 |
+
FILL_SHORT = b'\x80\x01'
|
| 66 |
+
FILL_INT = b'\x80\x00\x00\x01'
|
| 67 |
+
FILL_FLOAT = b'\x7C\xF0\x00\x00'
|
| 68 |
+
FILL_DOUBLE = b'\x47\x9E\x00\x00\x00\x00\x00\x00'
|
| 69 |
+
|
| 70 |
+
TYPEMAP = {NC_BYTE: ('b', 1),
|
| 71 |
+
NC_CHAR: ('c', 1),
|
| 72 |
+
NC_SHORT: ('h', 2),
|
| 73 |
+
NC_INT: ('i', 4),
|
| 74 |
+
NC_FLOAT: ('f', 4),
|
| 75 |
+
NC_DOUBLE: ('d', 8)}
|
| 76 |
+
|
| 77 |
+
FILLMAP = {NC_BYTE: FILL_BYTE,
|
| 78 |
+
NC_CHAR: FILL_CHAR,
|
| 79 |
+
NC_SHORT: FILL_SHORT,
|
| 80 |
+
NC_INT: FILL_INT,
|
| 81 |
+
NC_FLOAT: FILL_FLOAT,
|
| 82 |
+
NC_DOUBLE: FILL_DOUBLE}
|
| 83 |
+
|
| 84 |
+
REVERSE = {('b', 1): NC_BYTE,
|
| 85 |
+
('B', 1): NC_CHAR,
|
| 86 |
+
('c', 1): NC_CHAR,
|
| 87 |
+
('h', 2): NC_SHORT,
|
| 88 |
+
('i', 4): NC_INT,
|
| 89 |
+
('f', 4): NC_FLOAT,
|
| 90 |
+
('d', 8): NC_DOUBLE,
|
| 91 |
+
|
| 92 |
+
# these come from asarray(1).dtype.char and asarray('foo').dtype.char,
|
| 93 |
+
# used when getting the types from generic attributes.
|
| 94 |
+
('l', 4): NC_INT,
|
| 95 |
+
('S', 1): NC_CHAR}
|
| 96 |
+
|
| 97 |
+
|
| 98 |
+
class netcdf_file:
|
| 99 |
+
"""
|
| 100 |
+
A file object for NetCDF data.
|
| 101 |
+
|
| 102 |
+
A `netcdf_file` object has two standard attributes: `dimensions` and
|
| 103 |
+
`variables`. The values of both are dictionaries, mapping dimension
|
| 104 |
+
names to their associated lengths and variable names to variables,
|
| 105 |
+
respectively. Application programs should never modify these
|
| 106 |
+
dictionaries.
|
| 107 |
+
|
| 108 |
+
All other attributes correspond to global attributes defined in the
|
| 109 |
+
NetCDF file. Global file attributes are created by assigning to an
|
| 110 |
+
attribute of the `netcdf_file` object.
|
| 111 |
+
|
| 112 |
+
Parameters
|
| 113 |
+
----------
|
| 114 |
+
filename : string or file-like
|
| 115 |
+
string -> filename
|
| 116 |
+
mode : {'r', 'w', 'a'}, optional
|
| 117 |
+
read-write-append mode, default is 'r'
|
| 118 |
+
mmap : None or bool, optional
|
| 119 |
+
Whether to mmap `filename` when reading. Default is True
|
| 120 |
+
when `filename` is a file name, False when `filename` is a
|
| 121 |
+
file-like object. Note that when mmap is in use, data arrays
|
| 122 |
+
returned refer directly to the mmapped data on disk, and the
|
| 123 |
+
file cannot be closed as long as references to it exist.
|
| 124 |
+
version : {1, 2}, optional
|
| 125 |
+
version of netcdf to read / write, where 1 means *Classic
|
| 126 |
+
format* and 2 means *64-bit offset format*. Default is 1. See
|
| 127 |
+
`here <https://docs.unidata.ucar.edu/nug/current/netcdf_introduction.html#select_format>`__
|
| 128 |
+
for more info.
|
| 129 |
+
maskandscale : bool, optional
|
| 130 |
+
Whether to automatically scale and/or mask data based on attributes.
|
| 131 |
+
Default is False.
|
| 132 |
+
|
| 133 |
+
Notes
|
| 134 |
+
-----
|
| 135 |
+
The major advantage of this module over other modules is that it doesn't
|
| 136 |
+
require the code to be linked to the NetCDF libraries. This module is
|
| 137 |
+
derived from `pupynere <https://bitbucket.org/robertodealmeida/pupynere/>`_.
|
| 138 |
+
|
| 139 |
+
NetCDF files are a self-describing binary data format. The file contains
|
| 140 |
+
metadata that describes the dimensions and variables in the file. More
|
| 141 |
+
details about NetCDF files can be found `here
|
| 142 |
+
<https://www.unidata.ucar.edu/software/netcdf/guide_toc.html>`__. There
|
| 143 |
+
are three main sections to a NetCDF data structure:
|
| 144 |
+
|
| 145 |
+
1. Dimensions
|
| 146 |
+
2. Variables
|
| 147 |
+
3. Attributes
|
| 148 |
+
|
| 149 |
+
The dimensions section records the name and length of each dimension used
|
| 150 |
+
by the variables. The variables would then indicate which dimensions it
|
| 151 |
+
uses and any attributes such as data units, along with containing the data
|
| 152 |
+
values for the variable. It is good practice to include a
|
| 153 |
+
variable that is the same name as a dimension to provide the values for
|
| 154 |
+
that axes. Lastly, the attributes section would contain additional
|
| 155 |
+
information such as the name of the file creator or the instrument used to
|
| 156 |
+
collect the data.
|
| 157 |
+
|
| 158 |
+
When writing data to a NetCDF file, there is often the need to indicate the
|
| 159 |
+
'record dimension'. A record dimension is the unbounded dimension for a
|
| 160 |
+
variable. For example, a temperature variable may have dimensions of
|
| 161 |
+
latitude, longitude and time. If one wants to add more temperature data to
|
| 162 |
+
the NetCDF file as time progresses, then the temperature variable should
|
| 163 |
+
have the time dimension flagged as the record dimension.
|
| 164 |
+
|
| 165 |
+
In addition, the NetCDF file header contains the position of the data in
|
| 166 |
+
the file, so access can be done in an efficient manner without loading
|
| 167 |
+
unnecessary data into memory. It uses the ``mmap`` module to create
|
| 168 |
+
Numpy arrays mapped to the data on disk, for the same purpose.
|
| 169 |
+
|
| 170 |
+
Note that when `netcdf_file` is used to open a file with mmap=True
|
| 171 |
+
(default for read-only), arrays returned by it refer to data
|
| 172 |
+
directly on the disk. The file should not be closed, and cannot be cleanly
|
| 173 |
+
closed when asked, if such arrays are alive. You may want to copy data arrays
|
| 174 |
+
obtained from mmapped Netcdf file if they are to be processed after the file
|
| 175 |
+
is closed, see the example below.
|
| 176 |
+
|
| 177 |
+
Examples
|
| 178 |
+
--------
|
| 179 |
+
To create a NetCDF file:
|
| 180 |
+
|
| 181 |
+
>>> from scipy.io import netcdf_file
|
| 182 |
+
>>> import numpy as np
|
| 183 |
+
>>> f = netcdf_file('simple.nc', 'w')
|
| 184 |
+
>>> f.history = 'Created for a test'
|
| 185 |
+
>>> f.createDimension('time', 10)
|
| 186 |
+
>>> time = f.createVariable('time', 'i', ('time',))
|
| 187 |
+
>>> time[:] = np.arange(10)
|
| 188 |
+
>>> time.units = 'days since 2008-01-01'
|
| 189 |
+
>>> f.close()
|
| 190 |
+
|
| 191 |
+
Note the assignment of ``arange(10)`` to ``time[:]``. Exposing the slice
|
| 192 |
+
of the time variable allows for the data to be set in the object, rather
|
| 193 |
+
than letting ``arange(10)`` overwrite the ``time`` variable.
|
| 194 |
+
|
| 195 |
+
To read the NetCDF file we just created:
|
| 196 |
+
|
| 197 |
+
>>> from scipy.io import netcdf_file
|
| 198 |
+
>>> f = netcdf_file('simple.nc', 'r')
|
| 199 |
+
>>> print(f.history)
|
| 200 |
+
b'Created for a test'
|
| 201 |
+
>>> time = f.variables['time']
|
| 202 |
+
>>> print(time.units)
|
| 203 |
+
b'days since 2008-01-01'
|
| 204 |
+
>>> print(time.shape)
|
| 205 |
+
(10,)
|
| 206 |
+
>>> print(time[-1])
|
| 207 |
+
9
|
| 208 |
+
|
| 209 |
+
NetCDF files, when opened read-only, return arrays that refer
|
| 210 |
+
directly to memory-mapped data on disk:
|
| 211 |
+
|
| 212 |
+
>>> data = time[:]
|
| 213 |
+
|
| 214 |
+
If the data is to be processed after the file is closed, it needs
|
| 215 |
+
to be copied to main memory:
|
| 216 |
+
|
| 217 |
+
>>> data = time[:].copy()
|
| 218 |
+
>>> del time
|
| 219 |
+
>>> f.close()
|
| 220 |
+
>>> data.mean()
|
| 221 |
+
4.5
|
| 222 |
+
|
| 223 |
+
A NetCDF file can also be used as context manager:
|
| 224 |
+
|
| 225 |
+
>>> from scipy.io import netcdf_file
|
| 226 |
+
>>> with netcdf_file('simple.nc', 'r') as f:
|
| 227 |
+
... print(f.history)
|
| 228 |
+
b'Created for a test'
|
| 229 |
+
|
| 230 |
+
"""
|
| 231 |
+
def __init__(self, filename, mode='r', mmap=None, version=1,
|
| 232 |
+
maskandscale=False):
|
| 233 |
+
"""Initialize netcdf_file from fileobj (str or file-like)."""
|
| 234 |
+
if mode not in 'rwa':
|
| 235 |
+
raise ValueError("Mode must be either 'r', 'w' or 'a'.")
|
| 236 |
+
|
| 237 |
+
if hasattr(filename, 'seek'): # file-like
|
| 238 |
+
self.fp = filename
|
| 239 |
+
self.filename = 'None'
|
| 240 |
+
if mmap is None:
|
| 241 |
+
mmap = False
|
| 242 |
+
elif mmap and not hasattr(filename, 'fileno'):
|
| 243 |
+
raise ValueError('Cannot use file object for mmap')
|
| 244 |
+
else: # maybe it's a string
|
| 245 |
+
self.filename = filename
|
| 246 |
+
omode = 'r+' if mode == 'a' else mode
|
| 247 |
+
self.fp = open(self.filename, '%sb' % omode)
|
| 248 |
+
if mmap is None:
|
| 249 |
+
# Mmapped files on PyPy cannot be usually closed
|
| 250 |
+
# before the GC runs, so it's better to use mmap=False
|
| 251 |
+
# as the default.
|
| 252 |
+
mmap = (not IS_PYPY)
|
| 253 |
+
|
| 254 |
+
if mode != 'r':
|
| 255 |
+
# Cannot read write-only files
|
| 256 |
+
mmap = False
|
| 257 |
+
|
| 258 |
+
self.use_mmap = mmap
|
| 259 |
+
self.mode = mode
|
| 260 |
+
self.version_byte = version
|
| 261 |
+
self.maskandscale = maskandscale
|
| 262 |
+
|
| 263 |
+
self.dimensions = {}
|
| 264 |
+
self.variables = {}
|
| 265 |
+
|
| 266 |
+
self._dims = []
|
| 267 |
+
self._recs = 0
|
| 268 |
+
self._recsize = 0
|
| 269 |
+
|
| 270 |
+
self._mm = None
|
| 271 |
+
self._mm_buf = None
|
| 272 |
+
if self.use_mmap:
|
| 273 |
+
self._mm = mm.mmap(self.fp.fileno(), 0, access=mm.ACCESS_READ)
|
| 274 |
+
self._mm_buf = np.frombuffer(self._mm, dtype=np.int8)
|
| 275 |
+
|
| 276 |
+
self._attributes = {}
|
| 277 |
+
|
| 278 |
+
if mode in 'ra':
|
| 279 |
+
self._read()
|
| 280 |
+
|
| 281 |
+
def __setattr__(self, attr, value):
|
| 282 |
+
# Store user defined attributes in a separate dict,
|
| 283 |
+
# so we can save them to file later.
|
| 284 |
+
try:
|
| 285 |
+
self._attributes[attr] = value
|
| 286 |
+
except AttributeError:
|
| 287 |
+
pass
|
| 288 |
+
self.__dict__[attr] = value
|
| 289 |
+
|
| 290 |
+
def close(self):
|
| 291 |
+
"""Closes the NetCDF file."""
|
| 292 |
+
if hasattr(self, 'fp') and not self.fp.closed:
|
| 293 |
+
try:
|
| 294 |
+
self.flush()
|
| 295 |
+
finally:
|
| 296 |
+
self.variables = {}
|
| 297 |
+
if self._mm_buf is not None:
|
| 298 |
+
ref = weakref.ref(self._mm_buf)
|
| 299 |
+
self._mm_buf = None
|
| 300 |
+
if ref() is None:
|
| 301 |
+
# self._mm_buf is gc'd, and we can close the mmap
|
| 302 |
+
self._mm.close()
|
| 303 |
+
else:
|
| 304 |
+
# we cannot close self._mm, since self._mm_buf is
|
| 305 |
+
# alive and there may still be arrays referring to it
|
| 306 |
+
warnings.warn(
|
| 307 |
+
"Cannot close a netcdf_file opened with mmap=True, when "
|
| 308 |
+
"netcdf_variables or arrays referring to its data still "
|
| 309 |
+
"exist. All data arrays obtained from such files refer "
|
| 310 |
+
"directly to data on disk, and must be copied before the "
|
| 311 |
+
"file can be cleanly closed. "
|
| 312 |
+
"(See netcdf_file docstring for more information on mmap.)",
|
| 313 |
+
category=RuntimeWarning, stacklevel=2,
|
| 314 |
+
)
|
| 315 |
+
self._mm = None
|
| 316 |
+
self.fp.close()
|
| 317 |
+
__del__ = close
|
| 318 |
+
|
| 319 |
+
def __enter__(self):
|
| 320 |
+
return self
|
| 321 |
+
|
| 322 |
+
def __exit__(self, type, value, traceback):
|
| 323 |
+
self.close()
|
| 324 |
+
|
| 325 |
+
def createDimension(self, name, length):
|
| 326 |
+
"""
|
| 327 |
+
Adds a dimension to the Dimension section of the NetCDF data structure.
|
| 328 |
+
|
| 329 |
+
Note that this function merely adds a new dimension that the variables can
|
| 330 |
+
reference. The values for the dimension, if desired, should be added as
|
| 331 |
+
a variable using `createVariable`, referring to this dimension.
|
| 332 |
+
|
| 333 |
+
Parameters
|
| 334 |
+
----------
|
| 335 |
+
name : str
|
| 336 |
+
Name of the dimension (Eg, 'lat' or 'time').
|
| 337 |
+
length : int
|
| 338 |
+
Length of the dimension.
|
| 339 |
+
|
| 340 |
+
See Also
|
| 341 |
+
--------
|
| 342 |
+
createVariable
|
| 343 |
+
|
| 344 |
+
"""
|
| 345 |
+
if length is None and self._dims:
|
| 346 |
+
raise ValueError("Only first dimension may be unlimited!")
|
| 347 |
+
|
| 348 |
+
self.dimensions[name] = length
|
| 349 |
+
self._dims.append(name)
|
| 350 |
+
|
| 351 |
+
def createVariable(self, name, type, dimensions):
|
| 352 |
+
"""
|
| 353 |
+
Create an empty variable for the `netcdf_file` object, specifying its data
|
| 354 |
+
type and the dimensions it uses.
|
| 355 |
+
|
| 356 |
+
Parameters
|
| 357 |
+
----------
|
| 358 |
+
name : str
|
| 359 |
+
Name of the new variable.
|
| 360 |
+
type : dtype or str
|
| 361 |
+
Data type of the variable.
|
| 362 |
+
dimensions : sequence of str
|
| 363 |
+
List of the dimension names used by the variable, in the desired order.
|
| 364 |
+
|
| 365 |
+
Returns
|
| 366 |
+
-------
|
| 367 |
+
variable : netcdf_variable
|
| 368 |
+
The newly created ``netcdf_variable`` object.
|
| 369 |
+
This object has also been added to the `netcdf_file` object as well.
|
| 370 |
+
|
| 371 |
+
See Also
|
| 372 |
+
--------
|
| 373 |
+
createDimension
|
| 374 |
+
|
| 375 |
+
Notes
|
| 376 |
+
-----
|
| 377 |
+
Any dimensions to be used by the variable should already exist in the
|
| 378 |
+
NetCDF data structure or should be created by `createDimension` prior to
|
| 379 |
+
creating the NetCDF variable.
|
| 380 |
+
|
| 381 |
+
"""
|
| 382 |
+
shape = tuple([self.dimensions[dim] for dim in dimensions])
|
| 383 |
+
shape_ = tuple([dim or 0 for dim in shape]) # replace None with 0 for NumPy
|
| 384 |
+
|
| 385 |
+
type = dtype(type)
|
| 386 |
+
typecode, size = type.char, type.itemsize
|
| 387 |
+
if (typecode, size) not in REVERSE:
|
| 388 |
+
raise ValueError("NetCDF 3 does not support type %s" % type)
|
| 389 |
+
|
| 390 |
+
# convert to big endian always for NetCDF 3
|
| 391 |
+
data = empty(shape_, dtype=type.newbyteorder("B"))
|
| 392 |
+
self.variables[name] = netcdf_variable(
|
| 393 |
+
data, typecode, size, shape, dimensions,
|
| 394 |
+
maskandscale=self.maskandscale)
|
| 395 |
+
return self.variables[name]
|
| 396 |
+
|
| 397 |
+
def flush(self):
|
| 398 |
+
"""
|
| 399 |
+
Perform a sync-to-disk flush if the `netcdf_file` object is in write mode.
|
| 400 |
+
|
| 401 |
+
See Also
|
| 402 |
+
--------
|
| 403 |
+
sync : Identical function
|
| 404 |
+
|
| 405 |
+
"""
|
| 406 |
+
if hasattr(self, 'mode') and self.mode in 'wa':
|
| 407 |
+
self._write()
|
| 408 |
+
sync = flush
|
| 409 |
+
|
| 410 |
+
def _write(self):
|
| 411 |
+
self.fp.seek(0)
|
| 412 |
+
self.fp.write(b'CDF')
|
| 413 |
+
self.fp.write(array(self.version_byte, '>b').tobytes())
|
| 414 |
+
|
| 415 |
+
# Write headers and data.
|
| 416 |
+
self._write_numrecs()
|
| 417 |
+
self._write_dim_array()
|
| 418 |
+
self._write_gatt_array()
|
| 419 |
+
self._write_var_array()
|
| 420 |
+
|
| 421 |
+
def _write_numrecs(self):
|
| 422 |
+
# Get highest record count from all record variables.
|
| 423 |
+
for var in self.variables.values():
|
| 424 |
+
if var.isrec and len(var.data) > self._recs:
|
| 425 |
+
self.__dict__['_recs'] = len(var.data)
|
| 426 |
+
self._pack_int(self._recs)
|
| 427 |
+
|
| 428 |
+
def _write_dim_array(self):
|
| 429 |
+
if self.dimensions:
|
| 430 |
+
self.fp.write(NC_DIMENSION)
|
| 431 |
+
self._pack_int(len(self.dimensions))
|
| 432 |
+
for name in self._dims:
|
| 433 |
+
self._pack_string(name)
|
| 434 |
+
length = self.dimensions[name]
|
| 435 |
+
self._pack_int(length or 0) # replace None with 0 for record dimension
|
| 436 |
+
else:
|
| 437 |
+
self.fp.write(ABSENT)
|
| 438 |
+
|
| 439 |
+
def _write_gatt_array(self):
|
| 440 |
+
self._write_att_array(self._attributes)
|
| 441 |
+
|
| 442 |
+
def _write_att_array(self, attributes):
|
| 443 |
+
if attributes:
|
| 444 |
+
self.fp.write(NC_ATTRIBUTE)
|
| 445 |
+
self._pack_int(len(attributes))
|
| 446 |
+
for name, values in attributes.items():
|
| 447 |
+
self._pack_string(name)
|
| 448 |
+
self._write_att_values(values)
|
| 449 |
+
else:
|
| 450 |
+
self.fp.write(ABSENT)
|
| 451 |
+
|
| 452 |
+
def _write_var_array(self):
|
| 453 |
+
if self.variables:
|
| 454 |
+
self.fp.write(NC_VARIABLE)
|
| 455 |
+
self._pack_int(len(self.variables))
|
| 456 |
+
|
| 457 |
+
# Sort variable names non-recs first, then recs.
|
| 458 |
+
def sortkey(n):
|
| 459 |
+
v = self.variables[n]
|
| 460 |
+
if v.isrec:
|
| 461 |
+
return (-1,)
|
| 462 |
+
return v._shape
|
| 463 |
+
variables = sorted(self.variables, key=sortkey, reverse=True)
|
| 464 |
+
|
| 465 |
+
# Set the metadata for all variables.
|
| 466 |
+
for name in variables:
|
| 467 |
+
self._write_var_metadata(name)
|
| 468 |
+
# Now that we have the metadata, we know the vsize of
|
| 469 |
+
# each record variable, so we can calculate recsize.
|
| 470 |
+
self.__dict__['_recsize'] = sum([
|
| 471 |
+
var._vsize for var in self.variables.values()
|
| 472 |
+
if var.isrec])
|
| 473 |
+
# Set the data for all variables.
|
| 474 |
+
for name in variables:
|
| 475 |
+
self._write_var_data(name)
|
| 476 |
+
else:
|
| 477 |
+
self.fp.write(ABSENT)
|
| 478 |
+
|
| 479 |
+
def _write_var_metadata(self, name):
|
| 480 |
+
var = self.variables[name]
|
| 481 |
+
|
| 482 |
+
self._pack_string(name)
|
| 483 |
+
self._pack_int(len(var.dimensions))
|
| 484 |
+
for dimname in var.dimensions:
|
| 485 |
+
dimid = self._dims.index(dimname)
|
| 486 |
+
self._pack_int(dimid)
|
| 487 |
+
|
| 488 |
+
self._write_att_array(var._attributes)
|
| 489 |
+
|
| 490 |
+
nc_type = REVERSE[var.typecode(), var.itemsize()]
|
| 491 |
+
self.fp.write(nc_type)
|
| 492 |
+
|
| 493 |
+
if not var.isrec:
|
| 494 |
+
vsize = var.data.size * var.data.itemsize
|
| 495 |
+
vsize += -vsize % 4
|
| 496 |
+
else: # record variable
|
| 497 |
+
try:
|
| 498 |
+
vsize = var.data[0].size * var.data.itemsize
|
| 499 |
+
except IndexError:
|
| 500 |
+
vsize = 0
|
| 501 |
+
rec_vars = len([v for v in self.variables.values()
|
| 502 |
+
if v.isrec])
|
| 503 |
+
if rec_vars > 1:
|
| 504 |
+
vsize += -vsize % 4
|
| 505 |
+
self.variables[name].__dict__['_vsize'] = vsize
|
| 506 |
+
self._pack_int(vsize)
|
| 507 |
+
|
| 508 |
+
# Pack a bogus begin, and set the real value later.
|
| 509 |
+
self.variables[name].__dict__['_begin'] = self.fp.tell()
|
| 510 |
+
self._pack_begin(0)
|
| 511 |
+
|
| 512 |
+
def _write_var_data(self, name):
|
| 513 |
+
var = self.variables[name]
|
| 514 |
+
|
| 515 |
+
# Set begin in file header.
|
| 516 |
+
the_beguine = self.fp.tell()
|
| 517 |
+
self.fp.seek(var._begin)
|
| 518 |
+
self._pack_begin(the_beguine)
|
| 519 |
+
self.fp.seek(the_beguine)
|
| 520 |
+
|
| 521 |
+
# Write data.
|
| 522 |
+
if not var.isrec:
|
| 523 |
+
self.fp.write(var.data.tobytes())
|
| 524 |
+
count = var.data.size * var.data.itemsize
|
| 525 |
+
self._write_var_padding(var, var._vsize - count)
|
| 526 |
+
else: # record variable
|
| 527 |
+
# Handle rec vars with shape[0] < nrecs.
|
| 528 |
+
if self._recs > len(var.data):
|
| 529 |
+
shape = (self._recs,) + var.data.shape[1:]
|
| 530 |
+
# Resize in-place does not always work since
|
| 531 |
+
# the array might not be single-segment
|
| 532 |
+
try:
|
| 533 |
+
var.data.resize(shape)
|
| 534 |
+
except ValueError:
|
| 535 |
+
dtype = var.data.dtype
|
| 536 |
+
var.__dict__['data'] = np.resize(var.data, shape).astype(dtype)
|
| 537 |
+
|
| 538 |
+
pos0 = pos = self.fp.tell()
|
| 539 |
+
for rec in var.data:
|
| 540 |
+
# Apparently scalars cannot be converted to big endian. If we
|
| 541 |
+
# try to convert a ``=i4`` scalar to, say, '>i4' the dtype
|
| 542 |
+
# will remain as ``=i4``.
|
| 543 |
+
if not rec.shape and (rec.dtype.byteorder == '<' or
|
| 544 |
+
(rec.dtype.byteorder == '=' and LITTLE_ENDIAN)):
|
| 545 |
+
rec = rec.byteswap()
|
| 546 |
+
self.fp.write(rec.tobytes())
|
| 547 |
+
# Padding
|
| 548 |
+
count = rec.size * rec.itemsize
|
| 549 |
+
self._write_var_padding(var, var._vsize - count)
|
| 550 |
+
pos += self._recsize
|
| 551 |
+
self.fp.seek(pos)
|
| 552 |
+
self.fp.seek(pos0 + var._vsize)
|
| 553 |
+
|
| 554 |
+
def _write_var_padding(self, var, size):
|
| 555 |
+
encoded_fill_value = var._get_encoded_fill_value()
|
| 556 |
+
num_fills = size // len(encoded_fill_value)
|
| 557 |
+
self.fp.write(encoded_fill_value * num_fills)
|
| 558 |
+
|
| 559 |
+
def _write_att_values(self, values):
|
| 560 |
+
if hasattr(values, 'dtype'):
|
| 561 |
+
nc_type = REVERSE[values.dtype.char, values.dtype.itemsize]
|
| 562 |
+
else:
|
| 563 |
+
types = [(int, NC_INT), (float, NC_FLOAT), (str, NC_CHAR)]
|
| 564 |
+
|
| 565 |
+
# bytes index into scalars in py3k. Check for "string" types
|
| 566 |
+
if isinstance(values, (str, bytes)):
|
| 567 |
+
sample = values
|
| 568 |
+
else:
|
| 569 |
+
try:
|
| 570 |
+
sample = values[0] # subscriptable?
|
| 571 |
+
except TypeError:
|
| 572 |
+
sample = values # scalar
|
| 573 |
+
|
| 574 |
+
for class_, nc_type in types:
|
| 575 |
+
if isinstance(sample, class_):
|
| 576 |
+
break
|
| 577 |
+
|
| 578 |
+
typecode, size = TYPEMAP[nc_type]
|
| 579 |
+
dtype_ = '>%s' % typecode
|
| 580 |
+
# asarray() dies with bytes and '>c' in py3k. Change to 'S'
|
| 581 |
+
dtype_ = 'S' if dtype_ == '>c' else dtype_
|
| 582 |
+
|
| 583 |
+
values = asarray(values, dtype=dtype_)
|
| 584 |
+
|
| 585 |
+
self.fp.write(nc_type)
|
| 586 |
+
|
| 587 |
+
if values.dtype.char == 'S':
|
| 588 |
+
nelems = values.itemsize
|
| 589 |
+
else:
|
| 590 |
+
nelems = values.size
|
| 591 |
+
self._pack_int(nelems)
|
| 592 |
+
|
| 593 |
+
if not values.shape and (values.dtype.byteorder == '<' or
|
| 594 |
+
(values.dtype.byteorder == '=' and LITTLE_ENDIAN)):
|
| 595 |
+
values = values.byteswap()
|
| 596 |
+
self.fp.write(values.tobytes())
|
| 597 |
+
count = values.size * values.itemsize
|
| 598 |
+
self.fp.write(b'\x00' * (-count % 4)) # pad
|
| 599 |
+
|
| 600 |
+
def _read(self):
|
| 601 |
+
# Check magic bytes and version
|
| 602 |
+
magic = self.fp.read(3)
|
| 603 |
+
if not magic == b'CDF':
|
| 604 |
+
raise TypeError("Error: %s is not a valid NetCDF 3 file" %
|
| 605 |
+
self.filename)
|
| 606 |
+
self.__dict__['version_byte'] = frombuffer(self.fp.read(1), '>b')[0]
|
| 607 |
+
|
| 608 |
+
# Read file headers and set data.
|
| 609 |
+
self._read_numrecs()
|
| 610 |
+
self._read_dim_array()
|
| 611 |
+
self._read_gatt_array()
|
| 612 |
+
self._read_var_array()
|
| 613 |
+
|
| 614 |
+
def _read_numrecs(self):
|
| 615 |
+
self.__dict__['_recs'] = self._unpack_int()
|
| 616 |
+
|
| 617 |
+
def _read_dim_array(self):
|
| 618 |
+
header = self.fp.read(4)
|
| 619 |
+
if header not in [ZERO, NC_DIMENSION]:
|
| 620 |
+
raise ValueError("Unexpected header.")
|
| 621 |
+
count = self._unpack_int()
|
| 622 |
+
|
| 623 |
+
for dim in range(count):
|
| 624 |
+
name = self._unpack_string().decode('latin1')
|
| 625 |
+
length = self._unpack_int() or None # None for record dimension
|
| 626 |
+
self.dimensions[name] = length
|
| 627 |
+
self._dims.append(name) # preserve order
|
| 628 |
+
|
| 629 |
+
def _read_gatt_array(self):
|
| 630 |
+
for k, v in self._read_att_array().items():
|
| 631 |
+
self.__setattr__(k, v)
|
| 632 |
+
|
| 633 |
+
def _read_att_array(self):
|
| 634 |
+
header = self.fp.read(4)
|
| 635 |
+
if header not in [ZERO, NC_ATTRIBUTE]:
|
| 636 |
+
raise ValueError("Unexpected header.")
|
| 637 |
+
count = self._unpack_int()
|
| 638 |
+
|
| 639 |
+
attributes = {}
|
| 640 |
+
for attr in range(count):
|
| 641 |
+
name = self._unpack_string().decode('latin1')
|
| 642 |
+
attributes[name] = self._read_att_values()
|
| 643 |
+
return attributes
|
| 644 |
+
|
| 645 |
+
def _read_var_array(self):
|
| 646 |
+
header = self.fp.read(4)
|
| 647 |
+
if header not in [ZERO, NC_VARIABLE]:
|
| 648 |
+
raise ValueError("Unexpected header.")
|
| 649 |
+
|
| 650 |
+
begin = 0
|
| 651 |
+
dtypes = {'names': [], 'formats': []}
|
| 652 |
+
rec_vars = []
|
| 653 |
+
count = self._unpack_int()
|
| 654 |
+
for var in range(count):
|
| 655 |
+
(name, dimensions, shape, attributes,
|
| 656 |
+
typecode, size, dtype_, begin_, vsize) = self._read_var()
|
| 657 |
+
# https://www.unidata.ucar.edu/software/netcdf/guide_toc.html
|
| 658 |
+
# Note that vsize is the product of the dimension lengths
|
| 659 |
+
# (omitting the record dimension) and the number of bytes
|
| 660 |
+
# per value (determined from the type), increased to the
|
| 661 |
+
# next multiple of 4, for each variable. If a record
|
| 662 |
+
# variable, this is the amount of space per record. The
|
| 663 |
+
# netCDF "record size" is calculated as the sum of the
|
| 664 |
+
# vsize's of all the record variables.
|
| 665 |
+
#
|
| 666 |
+
# The vsize field is actually redundant, because its value
|
| 667 |
+
# may be computed from other information in the header. The
|
| 668 |
+
# 32-bit vsize field is not large enough to contain the size
|
| 669 |
+
# of variables that require more than 2^32 - 4 bytes, so
|
| 670 |
+
# 2^32 - 1 is used in the vsize field for such variables.
|
| 671 |
+
if shape and shape[0] is None: # record variable
|
| 672 |
+
rec_vars.append(name)
|
| 673 |
+
# The netCDF "record size" is calculated as the sum of
|
| 674 |
+
# the vsize's of all the record variables.
|
| 675 |
+
self.__dict__['_recsize'] += vsize
|
| 676 |
+
if begin == 0:
|
| 677 |
+
begin = begin_
|
| 678 |
+
dtypes['names'].append(name)
|
| 679 |
+
dtypes['formats'].append(str(shape[1:]) + dtype_)
|
| 680 |
+
|
| 681 |
+
# Handle padding with a virtual variable.
|
| 682 |
+
if typecode in 'bch':
|
| 683 |
+
actual_size = reduce(mul, (1,) + shape[1:]) * size
|
| 684 |
+
padding = -actual_size % 4
|
| 685 |
+
if padding:
|
| 686 |
+
dtypes['names'].append('_padding_%d' % var)
|
| 687 |
+
dtypes['formats'].append('(%d,)>b' % padding)
|
| 688 |
+
|
| 689 |
+
# Data will be set later.
|
| 690 |
+
data = None
|
| 691 |
+
else: # not a record variable
|
| 692 |
+
# Calculate size to avoid problems with vsize (above)
|
| 693 |
+
a_size = reduce(mul, shape, 1) * size
|
| 694 |
+
if self.use_mmap:
|
| 695 |
+
data = self._mm_buf[begin_:begin_+a_size].view(dtype=dtype_)
|
| 696 |
+
data.shape = shape
|
| 697 |
+
else:
|
| 698 |
+
pos = self.fp.tell()
|
| 699 |
+
self.fp.seek(begin_)
|
| 700 |
+
data = frombuffer(self.fp.read(a_size), dtype=dtype_
|
| 701 |
+
).copy()
|
| 702 |
+
data.shape = shape
|
| 703 |
+
self.fp.seek(pos)
|
| 704 |
+
|
| 705 |
+
# Add variable.
|
| 706 |
+
self.variables[name] = netcdf_variable(
|
| 707 |
+
data, typecode, size, shape, dimensions, attributes,
|
| 708 |
+
maskandscale=self.maskandscale)
|
| 709 |
+
|
| 710 |
+
if rec_vars:
|
| 711 |
+
# Remove padding when only one record variable.
|
| 712 |
+
if len(rec_vars) == 1:
|
| 713 |
+
dtypes['names'] = dtypes['names'][:1]
|
| 714 |
+
dtypes['formats'] = dtypes['formats'][:1]
|
| 715 |
+
|
| 716 |
+
# Build rec array.
|
| 717 |
+
if self.use_mmap:
|
| 718 |
+
buf = self._mm_buf[begin:begin+self._recs*self._recsize]
|
| 719 |
+
rec_array = buf.view(dtype=dtypes)
|
| 720 |
+
rec_array.shape = (self._recs,)
|
| 721 |
+
else:
|
| 722 |
+
pos = self.fp.tell()
|
| 723 |
+
self.fp.seek(begin)
|
| 724 |
+
rec_array = frombuffer(self.fp.read(self._recs*self._recsize),
|
| 725 |
+
dtype=dtypes).copy()
|
| 726 |
+
rec_array.shape = (self._recs,)
|
| 727 |
+
self.fp.seek(pos)
|
| 728 |
+
|
| 729 |
+
for var in rec_vars:
|
| 730 |
+
self.variables[var].__dict__['data'] = rec_array[var]
|
| 731 |
+
|
| 732 |
+
def _read_var(self):
|
| 733 |
+
name = self._unpack_string().decode('latin1')
|
| 734 |
+
dimensions = []
|
| 735 |
+
shape = []
|
| 736 |
+
dims = self._unpack_int()
|
| 737 |
+
|
| 738 |
+
for i in range(dims):
|
| 739 |
+
dimid = self._unpack_int()
|
| 740 |
+
dimname = self._dims[dimid]
|
| 741 |
+
dimensions.append(dimname)
|
| 742 |
+
dim = self.dimensions[dimname]
|
| 743 |
+
shape.append(dim)
|
| 744 |
+
dimensions = tuple(dimensions)
|
| 745 |
+
shape = tuple(shape)
|
| 746 |
+
|
| 747 |
+
attributes = self._read_att_array()
|
| 748 |
+
nc_type = self.fp.read(4)
|
| 749 |
+
vsize = self._unpack_int()
|
| 750 |
+
begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]()
|
| 751 |
+
|
| 752 |
+
typecode, size = TYPEMAP[nc_type]
|
| 753 |
+
dtype_ = '>%s' % typecode
|
| 754 |
+
|
| 755 |
+
return name, dimensions, shape, attributes, typecode, size, dtype_, begin, vsize
|
| 756 |
+
|
| 757 |
+
def _read_att_values(self):
|
| 758 |
+
nc_type = self.fp.read(4)
|
| 759 |
+
n = self._unpack_int()
|
| 760 |
+
|
| 761 |
+
typecode, size = TYPEMAP[nc_type]
|
| 762 |
+
|
| 763 |
+
count = n*size
|
| 764 |
+
values = self.fp.read(int(count))
|
| 765 |
+
self.fp.read(-count % 4) # read padding
|
| 766 |
+
|
| 767 |
+
if typecode != 'c':
|
| 768 |
+
values = frombuffer(values, dtype='>%s' % typecode).copy()
|
| 769 |
+
if values.shape == (1,):
|
| 770 |
+
values = values[0]
|
| 771 |
+
else:
|
| 772 |
+
values = values.rstrip(b'\x00')
|
| 773 |
+
return values
|
| 774 |
+
|
| 775 |
+
def _pack_begin(self, begin):
|
| 776 |
+
if self.version_byte == 1:
|
| 777 |
+
self._pack_int(begin)
|
| 778 |
+
elif self.version_byte == 2:
|
| 779 |
+
self._pack_int64(begin)
|
| 780 |
+
|
| 781 |
+
def _pack_int(self, value):
|
| 782 |
+
self.fp.write(array(value, '>i').tobytes())
|
| 783 |
+
_pack_int32 = _pack_int
|
| 784 |
+
|
| 785 |
+
def _unpack_int(self):
|
| 786 |
+
return int(frombuffer(self.fp.read(4), '>i')[0])
|
| 787 |
+
_unpack_int32 = _unpack_int
|
| 788 |
+
|
| 789 |
+
def _pack_int64(self, value):
|
| 790 |
+
self.fp.write(array(value, '>q').tobytes())
|
| 791 |
+
|
| 792 |
+
def _unpack_int64(self):
|
| 793 |
+
return frombuffer(self.fp.read(8), '>q')[0]
|
| 794 |
+
|
| 795 |
+
def _pack_string(self, s):
|
| 796 |
+
count = len(s)
|
| 797 |
+
self._pack_int(count)
|
| 798 |
+
self.fp.write(s.encode('latin1'))
|
| 799 |
+
self.fp.write(b'\x00' * (-count % 4)) # pad
|
| 800 |
+
|
| 801 |
+
def _unpack_string(self):
|
| 802 |
+
count = self._unpack_int()
|
| 803 |
+
s = self.fp.read(count).rstrip(b'\x00')
|
| 804 |
+
self.fp.read(-count % 4) # read padding
|
| 805 |
+
return s
|
| 806 |
+
|
| 807 |
+
|
| 808 |
+
class netcdf_variable:
|
| 809 |
+
"""
|
| 810 |
+
A data object for netcdf files.
|
| 811 |
+
|
| 812 |
+
`netcdf_variable` objects are constructed by calling the method
|
| 813 |
+
`netcdf_file.createVariable` on the `netcdf_file` object. `netcdf_variable`
|
| 814 |
+
objects behave much like array objects defined in numpy, except that their
|
| 815 |
+
data resides in a file. Data is read by indexing and written by assigning
|
| 816 |
+
to an indexed subset; the entire array can be accessed by the index ``[:]``
|
| 817 |
+
or (for scalars) by using the methods `getValue` and `assignValue`.
|
| 818 |
+
`netcdf_variable` objects also have attribute `shape` with the same meaning
|
| 819 |
+
as for arrays, but the shape cannot be modified. There is another read-only
|
| 820 |
+
attribute `dimensions`, whose value is the tuple of dimension names.
|
| 821 |
+
|
| 822 |
+
All other attributes correspond to variable attributes defined in
|
| 823 |
+
the NetCDF file. Variable attributes are created by assigning to an
|
| 824 |
+
attribute of the `netcdf_variable` object.
|
| 825 |
+
|
| 826 |
+
Parameters
|
| 827 |
+
----------
|
| 828 |
+
data : array_like
|
| 829 |
+
The data array that holds the values for the variable.
|
| 830 |
+
Typically, this is initialized as empty, but with the proper shape.
|
| 831 |
+
typecode : dtype character code
|
| 832 |
+
Desired data-type for the data array.
|
| 833 |
+
size : int
|
| 834 |
+
Desired element size for the data array.
|
| 835 |
+
shape : sequence of ints
|
| 836 |
+
The shape of the array. This should match the lengths of the
|
| 837 |
+
variable's dimensions.
|
| 838 |
+
dimensions : sequence of strings
|
| 839 |
+
The names of the dimensions used by the variable. Must be in the
|
| 840 |
+
same order of the dimension lengths given by `shape`.
|
| 841 |
+
attributes : dict, optional
|
| 842 |
+
Attribute values (any type) keyed by string names. These attributes
|
| 843 |
+
become attributes for the netcdf_variable object.
|
| 844 |
+
maskandscale : bool, optional
|
| 845 |
+
Whether to automatically scale and/or mask data based on attributes.
|
| 846 |
+
Default is False.
|
| 847 |
+
|
| 848 |
+
|
| 849 |
+
Attributes
|
| 850 |
+
----------
|
| 851 |
+
dimensions : list of str
|
| 852 |
+
List of names of dimensions used by the variable object.
|
| 853 |
+
isrec, shape
|
| 854 |
+
Properties
|
| 855 |
+
|
| 856 |
+
See also
|
| 857 |
+
--------
|
| 858 |
+
isrec, shape
|
| 859 |
+
|
| 860 |
+
"""
|
| 861 |
+
def __init__(self, data, typecode, size, shape, dimensions,
|
| 862 |
+
attributes=None,
|
| 863 |
+
maskandscale=False):
|
| 864 |
+
self.data = data
|
| 865 |
+
self._typecode = typecode
|
| 866 |
+
self._size = size
|
| 867 |
+
self._shape = shape
|
| 868 |
+
self.dimensions = dimensions
|
| 869 |
+
self.maskandscale = maskandscale
|
| 870 |
+
|
| 871 |
+
self._attributes = attributes or {}
|
| 872 |
+
for k, v in self._attributes.items():
|
| 873 |
+
self.__dict__[k] = v
|
| 874 |
+
|
| 875 |
+
def __setattr__(self, attr, value):
|
| 876 |
+
# Store user defined attributes in a separate dict,
|
| 877 |
+
# so we can save them to file later.
|
| 878 |
+
try:
|
| 879 |
+
self._attributes[attr] = value
|
| 880 |
+
except AttributeError:
|
| 881 |
+
pass
|
| 882 |
+
self.__dict__[attr] = value
|
| 883 |
+
|
| 884 |
+
def isrec(self):
|
| 885 |
+
"""Returns whether the variable has a record dimension or not.
|
| 886 |
+
|
| 887 |
+
A record dimension is a dimension along which additional data could be
|
| 888 |
+
easily appended in the netcdf data structure without much rewriting of
|
| 889 |
+
the data file. This attribute is a read-only property of the
|
| 890 |
+
`netcdf_variable`.
|
| 891 |
+
|
| 892 |
+
"""
|
| 893 |
+
return bool(self.data.shape) and not self._shape[0]
|
| 894 |
+
isrec = property(isrec)
|
| 895 |
+
|
| 896 |
+
def shape(self):
|
| 897 |
+
"""Returns the shape tuple of the data variable.
|
| 898 |
+
|
| 899 |
+
This is a read-only attribute and can not be modified in the
|
| 900 |
+
same manner of other numpy arrays.
|
| 901 |
+
"""
|
| 902 |
+
return self.data.shape
|
| 903 |
+
shape = property(shape)
|
| 904 |
+
|
| 905 |
+
def getValue(self):
|
| 906 |
+
"""
|
| 907 |
+
Retrieve a scalar value from a `netcdf_variable` of length one.
|
| 908 |
+
|
| 909 |
+
Raises
|
| 910 |
+
------
|
| 911 |
+
ValueError
|
| 912 |
+
If the netcdf variable is an array of length greater than one,
|
| 913 |
+
this exception will be raised.
|
| 914 |
+
|
| 915 |
+
"""
|
| 916 |
+
return self.data.item()
|
| 917 |
+
|
| 918 |
+
def assignValue(self, value):
|
| 919 |
+
"""
|
| 920 |
+
Assign a scalar value to a `netcdf_variable` of length one.
|
| 921 |
+
|
| 922 |
+
Parameters
|
| 923 |
+
----------
|
| 924 |
+
value : scalar
|
| 925 |
+
Scalar value (of compatible type) to assign to a length-one netcdf
|
| 926 |
+
variable. This value will be written to file.
|
| 927 |
+
|
| 928 |
+
Raises
|
| 929 |
+
------
|
| 930 |
+
ValueError
|
| 931 |
+
If the input is not a scalar, or if the destination is not a length-one
|
| 932 |
+
netcdf variable.
|
| 933 |
+
|
| 934 |
+
"""
|
| 935 |
+
if not self.data.flags.writeable:
|
| 936 |
+
# Work-around for a bug in NumPy. Calling itemset() on a read-only
|
| 937 |
+
# memory-mapped array causes a seg. fault.
|
| 938 |
+
# See NumPy ticket #1622, and SciPy ticket #1202.
|
| 939 |
+
# This check for `writeable` can be removed when the oldest version
|
| 940 |
+
# of NumPy still supported by scipy contains the fix for #1622.
|
| 941 |
+
raise RuntimeError("variable is not writeable")
|
| 942 |
+
|
| 943 |
+
self.data[:] = value
|
| 944 |
+
|
| 945 |
+
def typecode(self):
|
| 946 |
+
"""
|
| 947 |
+
Return the typecode of the variable.
|
| 948 |
+
|
| 949 |
+
Returns
|
| 950 |
+
-------
|
| 951 |
+
typecode : char
|
| 952 |
+
The character typecode of the variable (e.g., 'i' for int).
|
| 953 |
+
|
| 954 |
+
"""
|
| 955 |
+
return self._typecode
|
| 956 |
+
|
| 957 |
+
def itemsize(self):
|
| 958 |
+
"""
|
| 959 |
+
Return the itemsize of the variable.
|
| 960 |
+
|
| 961 |
+
Returns
|
| 962 |
+
-------
|
| 963 |
+
itemsize : int
|
| 964 |
+
The element size of the variable (e.g., 8 for float64).
|
| 965 |
+
|
| 966 |
+
"""
|
| 967 |
+
return self._size
|
| 968 |
+
|
| 969 |
+
def __getitem__(self, index):
|
| 970 |
+
if not self.maskandscale:
|
| 971 |
+
return self.data[index]
|
| 972 |
+
|
| 973 |
+
data = self.data[index].copy()
|
| 974 |
+
missing_value = self._get_missing_value()
|
| 975 |
+
data = self._apply_missing_value(data, missing_value)
|
| 976 |
+
scale_factor = self._attributes.get('scale_factor')
|
| 977 |
+
add_offset = self._attributes.get('add_offset')
|
| 978 |
+
if add_offset is not None or scale_factor is not None:
|
| 979 |
+
data = data.astype(np.float64)
|
| 980 |
+
if scale_factor is not None:
|
| 981 |
+
data = data * scale_factor
|
| 982 |
+
if add_offset is not None:
|
| 983 |
+
data += add_offset
|
| 984 |
+
|
| 985 |
+
return data
|
| 986 |
+
|
| 987 |
+
def __setitem__(self, index, data):
|
| 988 |
+
if self.maskandscale:
|
| 989 |
+
missing_value = (
|
| 990 |
+
self._get_missing_value() or
|
| 991 |
+
getattr(data, 'fill_value', 999999))
|
| 992 |
+
self._attributes.setdefault('missing_value', missing_value)
|
| 993 |
+
self._attributes.setdefault('_FillValue', missing_value)
|
| 994 |
+
data = ((data - self._attributes.get('add_offset', 0.0)) /
|
| 995 |
+
self._attributes.get('scale_factor', 1.0))
|
| 996 |
+
data = np.ma.asarray(data).filled(missing_value)
|
| 997 |
+
if self._typecode not in 'fd' and data.dtype.kind == 'f':
|
| 998 |
+
data = np.round(data)
|
| 999 |
+
|
| 1000 |
+
# Expand data for record vars?
|
| 1001 |
+
if self.isrec:
|
| 1002 |
+
if isinstance(index, tuple):
|
| 1003 |
+
rec_index = index[0]
|
| 1004 |
+
else:
|
| 1005 |
+
rec_index = index
|
| 1006 |
+
if isinstance(rec_index, slice):
|
| 1007 |
+
recs = (rec_index.start or 0) + len(data)
|
| 1008 |
+
else:
|
| 1009 |
+
recs = rec_index + 1
|
| 1010 |
+
if recs > len(self.data):
|
| 1011 |
+
shape = (recs,) + self._shape[1:]
|
| 1012 |
+
# Resize in-place does not always work since
|
| 1013 |
+
# the array might not be single-segment
|
| 1014 |
+
try:
|
| 1015 |
+
self.data.resize(shape)
|
| 1016 |
+
except ValueError:
|
| 1017 |
+
dtype = self.data.dtype
|
| 1018 |
+
self.__dict__['data'] = np.resize(self.data, shape).astype(dtype)
|
| 1019 |
+
self.data[index] = data
|
| 1020 |
+
|
| 1021 |
+
def _default_encoded_fill_value(self):
|
| 1022 |
+
"""
|
| 1023 |
+
The default encoded fill-value for this Variable's data type.
|
| 1024 |
+
"""
|
| 1025 |
+
nc_type = REVERSE[self.typecode(), self.itemsize()]
|
| 1026 |
+
return FILLMAP[nc_type]
|
| 1027 |
+
|
| 1028 |
+
def _get_encoded_fill_value(self):
|
| 1029 |
+
"""
|
| 1030 |
+
Returns the encoded fill value for this variable as bytes.
|
| 1031 |
+
|
| 1032 |
+
This is taken from either the _FillValue attribute, or the default fill
|
| 1033 |
+
value for this variable's data type.
|
| 1034 |
+
"""
|
| 1035 |
+
if '_FillValue' in self._attributes:
|
| 1036 |
+
fill_value = np.array(self._attributes['_FillValue'],
|
| 1037 |
+
dtype=self.data.dtype).tobytes()
|
| 1038 |
+
if len(fill_value) == self.itemsize():
|
| 1039 |
+
return fill_value
|
| 1040 |
+
else:
|
| 1041 |
+
return self._default_encoded_fill_value()
|
| 1042 |
+
else:
|
| 1043 |
+
return self._default_encoded_fill_value()
|
| 1044 |
+
|
| 1045 |
+
def _get_missing_value(self):
|
| 1046 |
+
"""
|
| 1047 |
+
Returns the value denoting "no data" for this variable.
|
| 1048 |
+
|
| 1049 |
+
If this variable does not have a missing/fill value, returns None.
|
| 1050 |
+
|
| 1051 |
+
If both _FillValue and missing_value are given, give precedence to
|
| 1052 |
+
_FillValue. The netCDF standard gives special meaning to _FillValue;
|
| 1053 |
+
missing_value is just used for compatibility with old datasets.
|
| 1054 |
+
"""
|
| 1055 |
+
|
| 1056 |
+
if '_FillValue' in self._attributes:
|
| 1057 |
+
missing_value = self._attributes['_FillValue']
|
| 1058 |
+
elif 'missing_value' in self._attributes:
|
| 1059 |
+
missing_value = self._attributes['missing_value']
|
| 1060 |
+
else:
|
| 1061 |
+
missing_value = None
|
| 1062 |
+
|
| 1063 |
+
return missing_value
|
| 1064 |
+
|
| 1065 |
+
@staticmethod
|
| 1066 |
+
def _apply_missing_value(data, missing_value):
|
| 1067 |
+
"""
|
| 1068 |
+
Applies the given missing value to the data array.
|
| 1069 |
+
|
| 1070 |
+
Returns a numpy.ma array, with any value equal to missing_value masked
|
| 1071 |
+
out (unless missing_value is None, in which case the original array is
|
| 1072 |
+
returned).
|
| 1073 |
+
"""
|
| 1074 |
+
|
| 1075 |
+
if missing_value is None:
|
| 1076 |
+
newdata = data
|
| 1077 |
+
else:
|
| 1078 |
+
try:
|
| 1079 |
+
missing_value_isnan = np.isnan(missing_value)
|
| 1080 |
+
except (TypeError, NotImplementedError):
|
| 1081 |
+
# some data types (e.g., characters) cannot be tested for NaN
|
| 1082 |
+
missing_value_isnan = False
|
| 1083 |
+
|
| 1084 |
+
if missing_value_isnan:
|
| 1085 |
+
mymask = np.isnan(data)
|
| 1086 |
+
else:
|
| 1087 |
+
mymask = (data == missing_value)
|
| 1088 |
+
|
| 1089 |
+
newdata = np.ma.masked_where(mymask, data)
|
| 1090 |
+
|
| 1091 |
+
return newdata
|
| 1092 |
+
|
| 1093 |
+
|
| 1094 |
+
NetCDFFile = netcdf_file
|
| 1095 |
+
NetCDFVariable = netcdf_variable
|
videochat2/lib/python3.10/site-packages/scipy/io/_test_fortran.cpython-310-x86_64-linux-gnu.so
ADDED
|
Binary file (63.4 kB). View file
|
|
|
videochat2/lib/python3.10/site-packages/scipy/io/harwell_boeing.py
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# This file is not meant for public use and will be removed in SciPy v2.0.0.
|
| 2 |
+
# Use the `scipy.io` namespace for importing the functions
|
| 3 |
+
# included below.
|
| 4 |
+
|
| 5 |
+
from scipy._lib.deprecation import _sub_module_deprecation
|
| 6 |
+
|
| 7 |
+
__all__ = [ # noqa: F822
|
| 8 |
+
'MalformedHeader', 'hb_read', 'hb_write', 'HBInfo',
|
| 9 |
+
'HBFile', 'HBMatrixType', 'FortranFormatParser', 'IntFormat',
|
| 10 |
+
'ExpFormat', 'BadFortranFormat', 'hb'
|
| 11 |
+
]
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
def __dir__():
|
| 15 |
+
return __all__
|
| 16 |
+
|
| 17 |
+
|
| 18 |
+
def __getattr__(name):
|
| 19 |
+
return _sub_module_deprecation(sub_package="io", module="harwell_boeing",
|
| 20 |
+
private_modules=["_harwell_boeing"], all=__all__,
|
| 21 |
+
attribute=name)
|
videochat2/lib/python3.10/site-packages/scipy/io/idl.py
ADDED
|
@@ -0,0 +1,20 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# This file is not meant for public use and will be removed in SciPy v2.0.0.
|
| 2 |
+
# Use the `scipy.io` namespace for importing the functions
|
| 3 |
+
# included below.
|
| 4 |
+
|
| 5 |
+
from scipy._lib.deprecation import _sub_module_deprecation
|
| 6 |
+
|
| 7 |
+
__all__ = [ # noqa: F822
|
| 8 |
+
'readsav', 'DTYPE_DICT', 'RECTYPE_DICT', 'STRUCT_DICT',
|
| 9 |
+
'Pointer', 'ObjectPointer', 'AttrDict'
|
| 10 |
+
]
|
| 11 |
+
|
| 12 |
+
|
| 13 |
+
def __dir__():
|
| 14 |
+
return __all__
|
| 15 |
+
|
| 16 |
+
|
| 17 |
+
def __getattr__(name):
|
| 18 |
+
return _sub_module_deprecation(sub_package="io", module="idl",
|
| 19 |
+
private_modules=["_idl"], all=__all__,
|
| 20 |
+
attribute=name)
|
videochat2/lib/python3.10/site-packages/scipy/io/mmio.py
ADDED
|
@@ -0,0 +1,20 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# This file is not meant for public use and will be removed in SciPy v2.0.0.
|
| 2 |
+
# Use the `scipy.io` namespace for importing the functions
|
| 3 |
+
# included below.
|
| 4 |
+
|
| 5 |
+
from scipy._lib.deprecation import _sub_module_deprecation
|
| 6 |
+
|
| 7 |
+
__all__ = [ # noqa: F822
|
| 8 |
+
'mminfo', 'mmread', 'mmwrite', 'MMFile',
|
| 9 |
+
'coo_matrix', 'asstr'
|
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+
]
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+
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+
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+
def __dir__():
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+
return __all__
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+
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+
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+
def __getattr__(name):
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+
return _sub_module_deprecation(sub_package="io", module="mmio",
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+
private_modules=["_mmio"], all=__all__,
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+
attribute=name)
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videochat2/lib/python3.10/site-packages/scipy/io/netcdf.py
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+
# This file is not meant for public use and will be removed in SciPy v2.0.0.
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+
# Use the `scipy.io` namespace for importing the functions
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+
# included below.
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+
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+
from scipy._lib.deprecation import _sub_module_deprecation
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+
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| 7 |
+
__all__ = [ # noqa: F822
|
| 8 |
+
'netcdf_file', 'netcdf_variable',
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| 9 |
+
'array', 'LITTLE_ENDIAN', 'IS_PYPY', 'ABSENT', 'ZERO',
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+
'NC_BYTE', 'NC_CHAR', 'NC_SHORT', 'NC_INT', 'NC_FLOAT',
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+
'NC_DOUBLE', 'NC_DIMENSION', 'NC_VARIABLE', 'NC_ATTRIBUTE',
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| 12 |
+
'FILL_BYTE', 'FILL_CHAR', 'FILL_SHORT', 'FILL_INT', 'FILL_FLOAT',
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| 13 |
+
'FILL_DOUBLE', 'TYPEMAP', 'FILLMAP', 'REVERSE', 'NetCDFFile',
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+
'NetCDFVariable'
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+
]
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+
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+
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+
def __dir__():
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+
return __all__
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+
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+
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+
def __getattr__(name):
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| 23 |
+
return _sub_module_deprecation(sub_package="io", module="netcdf",
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| 24 |
+
private_modules=["_netcdf"], all=__all__,
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+
attribute=name)
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videochat2/lib/python3.10/site-packages/scipy/io/tests/__init__.py
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videochat2/lib/python3.10/site-packages/scipy/io/tests/__pycache__/__init__.cpython-310.pyc
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