1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271
|
# -*- coding: utf-8 -*-
# Copyright 2007-2023 The HyperSpy developers
#
# This file is part of RosettaSciIO.
#
# RosettaSciIO is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# RosettaSciIO is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with RosettaSciIO. If not, see <https://www.gnu.org/licenses/#GPL>.
import logging
import os
from collections.abc import Iterable
import imageio.v3 as iio
import numpy as np
from PIL import Image
from rsciio._docstrings import (
FILENAME_DOC,
LAZY_DOC,
RETURNS_DOC,
SIGNAL_DOC,
)
from rsciio.utils.image import _parse_axes_from_metadata, _parse_exif_tags
from rsciio.utils.tools import _UREG
_logger = logging.getLogger(__name__)
def file_writer(
filename,
signal,
scalebar=False,
scalebar_kwds=None,
output_size=None,
imshow_kwds=None,
**kwds,
):
"""
Write data to any format supported by pillow.
The file format is defined by the file extension that is any one
supported by imageio. When any of the parameters ``output_size``,
``scalebar`` or ``imshow_kwds`` is given,
:py:func:`~.matplotlib.pyplot.imshow` is used to generate a figure.
Parameters
----------
%s
%s
scalebar : bool, Default=False
Export the image with a scalebar.
scalebar_kwds : dict, optional
Dictionary of keyword arguments for the scalebar. Useful to set
formatting, location, etc. of the scalebar. See the documentation of
the 'matplotlib-scalebar' library for more information.
output_size : {2-tuple, int, None}, Default=None
The output size of the image in pixels (width, height):
* if ``int``, defines the width of the image, the height is
determined from the aspect ratio of the image
* if ``2-tuple``, defines the width and height of the
image. Padding with white pixels is used to maintain the aspect
ratio of the image.
* if ``None``, the size of the data is used.
For output sizes larger than the data size, "nearest" interpolation is
used by default and this behaviour can be changed through the
``imshow_kwds`` dictionary.
imshow_kwds : dict, optional
Keyword arguments dictionary for :py:func:`~.matplotlib.pyplot.imshow`.
**kwds : dict, optional
Allows to pass keyword arguments supported by the individual file
writers as documented at
https://imageio.readthedocs.io/en/stable/formats/index.html when
exporting an image without scalebar. When exporting with a scalebar,
the keyword arguments are passed to the `pil_kwargs` dictionary of
:py:func:`~matplotlib.pyplot.savefig`.
"""
data = signal["data"]
sig_axes = [ax for ax in signal["axes"] if not ax["navigate"]]
nav_axes = [ax for ax in signal["axes"] if ax["navigate"]]
if scalebar_kwds is None:
scalebar_kwds = dict()
scalebar_kwds.setdefault("box_alpha", 0.75)
scalebar_kwds.setdefault("location", "lower left")
# HyperSpy uses struct arrays to store RGBA data
from rsciio.utils import rgb_tools
if rgb_tools.is_rgbx(data):
data = rgb_tools.rgbx2regular_array(data)
if scalebar:
try:
from matplotlib_scalebar.scalebar import ScaleBar
except ImportError: # pragma: no cover
scalebar = False
_logger.warning(
"Exporting image with scalebar requires the "
"matplotlib-scalebar library."
)
if scalebar or output_size or imshow_kwds:
try:
from matplotlib.figure import Figure
except ImportError:
raise ValueError(
"Using the `output_size`, `imshow_kwds` arguments or "
"exporting with a scalebar requires the matplotlib library."
)
dpi = 100
if imshow_kwds is None:
imshow_kwds = dict()
imshow_kwds.setdefault("cmap", "gray")
axes = []
if len(sig_axes) == 2:
axes = sig_axes
elif len(nav_axes) == 2:
# Use navigation axes
axes = nav_axes
else:
raise RuntimeError("This dimensionality is not supported.")
aspect_ratio = imshow_kwds.get("aspect", 1)
if output_size is None:
# fall back to image size taking into account aspect
ratio = (1, aspect_ratio)
output_size = [axis["size"] * r for axis, r in zip(axes[::-1], ratio)]
elif isinstance(output_size, (int, float)):
aspect_ratio *= data.shape[0] / data.shape[1]
output_size = [output_size, output_size * aspect_ratio]
elif isinstance(output_size, Iterable) and len(output_size) != 2:
# Catch error here, because matplotlib error is not obvious
raise ValueError("If `output_size` is an iterable, it must be of length 2.")
fig = Figure(figsize=[size / dpi for size in output_size], dpi=dpi)
# List of format supported by matplotlib
supported_format = sorted(fig.canvas.get_supported_filetypes())
if os.path.splitext(filename)[1].replace(".", "") not in supported_format:
if scalebar:
raise ValueError(
"Exporting image with scalebar is supported "
f"only with {', '.join(supported_format)}."
)
if output_size:
raise ValueError(
"Setting the output size is only supported "
f"with {', '.join(supported_format)}."
)
if scalebar:
# Sanity check of the axes
# This plugin doesn't support non-uniform axes, we don't need to check
# if the axes have a scale attribute
if axes[0]["scale"] != axes[1]["scale"] or axes[0]["units"] != axes[1]["units"]:
raise ValueError(
"Scale and units must be the same for each axes "
"to export images with a scale bar."
)
if scalebar or output_size:
ax = fig.add_axes([0, 0, 1, 1])
ax.axis("off")
ax.imshow(data, **imshow_kwds)
if scalebar:
# Add scalebar
axis = axes[0]
units = axis["units"]
if units is None:
units = "px"
scalebar_kwds["dimension"] = "pixel-length"
else:
units = _UREG.Quantity(units)
if units.check("1/[length]"):
scalebar_kwds["dimension"] = "si-length-reciprocal"
# Standard formatting of units to avoid issue with
# matplotlib-scalebar
units = f"{units.units:~C}"
ax.add_artist(ScaleBar(axis["scale"], units, **scalebar_kwds))
fig.savefig(filename, dpi=dpi, pil_kwargs=kwds)
else:
iio.imwrite(filename, data, **kwds)
file_writer.__doc__ %= (FILENAME_DOC.replace("read", "write to"), SIGNAL_DOC)
def file_reader(filename, lazy=False, **kwds):
"""
Read data from any format supported by imageio (PIL/pillow).
The file format is defined by the file extension that is any one supported by
imageio. For a list of formats see
https://imageio.readthedocs.io/en/stable/formats/index.html.
Parameters
----------
%s
%s
**kwds : dict, optional
Allows to pass keyword arguments supported by the individual file
readers as documented at
https://imageio.readthedocs.io/en/stable/formats/index.html.
%s
"""
if lazy:
# load the image fully to check the dtype and shape, should be cheap.
# Then store this info for later re-loading when required
from dask import delayed
from dask.array import from_delayed
val = delayed(_read_data, pure=True)(filename, **kwds)
dc = from_delayed(val, shape=val.shape, dtype=val.dtype)
else:
dc = _read_data(filename, **kwds)
om = {}
im = Image.open(filename)
om["exif_tags"] = _parse_exif_tags(im)
axes = _parse_axes_from_metadata(om["exif_tags"], dc.shape)
return [
{
"data": dc,
"axes": axes,
"metadata": {
"General": {"original_filename": os.path.split(filename)[1]},
"Signal": {"signal_type": ""},
},
"original_metadata": om,
}
]
file_reader.__doc__ %= (FILENAME_DOC, LAZY_DOC, RETURNS_DOC)
def _read_data(filename, **kwds):
dc = np.squeeze(iio.imread(filename))
if len(dc.shape) > 2:
# It may be a grayscale image that was saved in the RGB or RGBA
# format
if (dc[:, :, 1] == dc[:, :, 2]).all() and (dc[:, :, 1] == dc[:, :, 2]).all():
dc = dc[:, :, 0]
else:
# HyperSpy uses struct arrays to store RGB data
from rsciio.utils import rgb_tools
dc = rgb_tools.regular_array2rgbx(dc)
return dc
|