# coding: utf-8
from typing import Optional, Callable, Union, Tuple, Iterable
import numpy as np
from pathlib import Path
from .camera_processes import DICVEProcess
from .camera import Camera
from ..tool.camera_config import DICVEConfig, SpotsBoxes
from .._global import CameraConfigError
[docs]
class DICVE(Camera):
"""This Block can perform video-extensometry on images acquired by a
:class:`~crappy.camera.Camera` object, by tracking patches using Digital
Image Correlation techniques.
It takes no input :class:`~crappy.links.Link` in a majority of situations,
and outputs the results of the video-extensometry. It is a subclass of the
:class:`~crappy.blocks.Camera` Block, and inherits of all its features. That
includes the possibility to record and to display images in real-time,
simultaneously to the image acquisition and processing. Refer to the
documentation of the Camera Block for more information on these features.
This Block is quite similar to the :class:`~crappy.blocks.VideoExtenso`
Block, except this latter tracks spots instead of patches with a texture.
Both Blocks output similar information, although the default labels and the
data format are slightly different. The :class:`~crappy.blocks.DISCorrel`
Block also relies on image correlation techniques for estimating the
strain and the displacement on acquired images, but it only performs
correlation on a single patch and is designed to have a much greater
accuracy on this single patch. The :class:`~crappy.blocks.GPUVE` Block also
performs video-extensometry based on digital image correlation, but the
correlation is GPU-accelerated. The algorithm used for the correlation is
also different from the ones available in this Block.
For tracking the provided patches, several image correlation techniques are
available. The most effective one is DISFlow, for which many parameters can
be tuned. The other techniques are lighter on the CPU but also less precise.
For each image, several values are computed and sent to the downstream
Blocks. See the ``labels`` argument for a complete list.
Similar to the :class:`~crappy.tool.camera_config.CameraConfig` window that
can be displayed by the Camera Block, this Block can display a
:class:`~crappy.tool.camera_config.DICVEConfig` window before the test
starts. Here, the user can also select the patches to track if they were not
already specified as an argument.
.. versionadded:: 1.4.0
.. versionchanged:: 2.0.0 renamed from *DISVE* to *DICVE*
"""
[docs]
def __init__(self,
camera: str,
transform: Optional[Callable[[np.ndarray], np.ndarray]] = None,
config: bool = True,
display_images: bool = False,
displayer_backend: Optional[str] = None,
displayer_framerate: float = 5,
software_trig_label: Optional[str] = None,
display_freq: bool = False,
freq: Optional[float] = 200,
debug: Optional[bool] = False,
save_images: bool = False,
img_extension: str = "tiff",
save_folder: Optional[Union[str, Path]] = None,
save_period: int = 1,
save_backend: Optional[str] = None,
image_generator: Optional[Callable[[float, float],
np.ndarray]] = None,
img_shape: Optional[Tuple[int, int]] = None,
img_dtype: Optional[str] = None,
patches: Optional[Iterable[Tuple[int, int, int, int]]] = None,
labels: Optional[Union[str, Iterable[str]]] = None,
method: str = 'Disflow',
alpha: float = 3,
delta: float = 1,
gamma: float = 0,
finest_scale: int = 1,
iterations: int = 1,
gradient_iterations: int = 10,
patch_size: int = 8,
patch_stride: int = 3,
border: float = 0.2,
safe: bool = True,
follow: bool = True,
raise_on_patch_exit: bool = True,
**kwargs) -> None:
"""Sets the arguments and initializes the parent class.
Args:
camera: The name of the :class:`~crappy.camera.Camera` object to use for
acquiring the images. Arguments can be passed to this Camera as
``kwargs`` of this Block. This argument is ignored if the
``image_generator`` argument is provided.
transform: A callable taking an image as an argument, and returning a
transformed image as an output. Allows applying a post-processing
operation to the acquired images. This is done right after the
acquisition, so the original image is permanently lost and only the
transformed image is displayed and/or saved and/or further processed.
The transform operation is not parallelized, so it might negatively
affect the acquisition framerate if it is too heavy.
.. versionadded:: 1.5.10
config: If :obj:`True`, a
:class:`~crappy.tool.camera_config.DICVEConfig` window is displayed
before the test starts. There, the user can interactively adjust the
different
:class:`~crappy.camera.meta_camera.camera_setting.CameraSetting`
available for the selected :class:`~crappy.camera.Camera`, visualize
the acquired images, and select the patches to track if they haven't
been given in the ``patches`` argument. The test starts when closing
the configuration window. If not enabled, the ``img_dtype``,
``img_shape`` and ``patches`` arguments must be provided.
.. versionadded:: 1.5.10
display_images: If :obj:`True`, displays the acquired images in a
dedicated window, using the backend given in ``displayer_backend`` and
at the frequency specified in ``displayer_framerate``. This option
should be considered as a debug or basic follow-up feature, it is not
intended to be very fast nor to display high-quality images. The
maximum resolution of the displayed images in `640x480`, the images
might be downscaled to fit in this format. In addition to the acquired
frames, the tracked patches are also displayed on the image as an
overlay.
.. versionchanged:: 1.5.10
renamed from *show_image* to *display_images*
displayer_backend: The backend to use for displaying the images. Can be
either ``'cv2'`` or ``'mpl'``, to use respectively :mod:`cv2` (OpenCV)
or :mod:`matplotlib`. ``'cv2'`` usually allows achieving a higher
display frequency. Ignored if ``display_images`` is :obj:`False`. If
not given and ``display_images`` is :obj:`True`, ``'cv2'`` is tried
first and ``'mpl'`` second, and the first available one is used.
.. versionadded:: 1.5.10
displayer_framerate: The maximum update frequency of the image displayer,
as an :obj:`int`. This value usually lies between 5 and 30Hz, the
default is 5. The achieved update frequency might be lower than
requested. Ignored if ``display_images`` is :obj:`False`.
.. versionadded:: 1.5.10
software_trig_label: The name of a label used as a software trigger for
the :class:`~crappy.camera.Camera`. If given, images will only be
acquired when receiving data over this label. The received value does
not matter. This software trigger is not meant to be very precise, it
is recommended not to rely on it for a trigger frequency greater than
10Hz, in which case a hardware trigger should be preferred if available
on the camera.
.. versionadded:: 2.0.0
display_freq: If :obj:`True`, displays the looping frequency of the
Block.
.. versionchanged:: 2.0.0 renamed from *verbose* to *display_freq*
debug: If :obj:`True`, displays all the log messages including the
:obj:`~logging.DEBUG` ones. If :obj:`False`, only displays the log
messages with :obj:`~logging.INFO` level or higher. If :obj:`None`,
disables logging for this Block.
.. versionadded:: 2.0.0
freq: The target looping frequency for the Block. If :obj:`None`, loops
as fast as possible.
.. versionadded:: 1.5.10
save_images: If :obj:`True`, the acquired images are saved to the folder
specified in ``save_folder``, in the format specified in
``img_extension``, using the backend specified in ``save_backend``, and
at the frequency specified in ``save_period``. Each image is saved with
the name : ``<frame_nr>_<timestamp>.<extension>``, and can thus easily
be identified. Along with the images, a ``metadata.csv`` file records
the metadata of all the saved images. This metadata is either the one
returned by the :meth:`~crappy.camera.Camera.get_image` method of the
:class:`~crappy.camera.Camera` object, or the default one generated in
the :meth:`~crappy.blocks.Camera.loop` method of the
:class:`~crappy.blocks.Camera` Block. Depending on the framerate of the
camera and the performance of the computer, it is not guaranteed that
all the acquired images will be recorded.
.. versionadded:: 1.5.10
img_extension: The file extension for the recorded images, as a
:obj:`str` and without the dot. Common file extensions include `tiff`,
`png`, `jpg`, etc. Depending on the used ``save_backend``, some
extensions might not be available. It is currently not possible to
customize the save parameters further than choosing the file extension.
Ignored if ``save_images`` is :obj:`False`.
.. versionadded:: 2.0.0
save_folder: Path to the folder where to save the images, either as a
:obj:`str` or as a :obj:`pathlib.Path`. Can be an absolute or a
relative path, pointing to a folder. If the folder does not exist, it
will be created (if the user has permission). If the given folder
already contains a ``metadata.csv`` file (and thus likely images from
Crappy), images are saved to another folder with the same name except
a suffix is appended. Ignored if ``save_images`` is :obj:`False`. If
not provided and ``save_images`` is :obj:`True`, the images are saved
to the folder ``Crappy_images``, created next to the running script.
.. versionadded:: 1.5.10
save_period: Must be given as an :obj:`int`. Only one out of that number
images at most will be saved. Allows to have a known periodicity in
case the framerate is too high to record all the images. Or simply to
reduce the number of recorded images if saving them all is not needed.
Ignored if ``save_images`` is :obj:`False`.
.. versionadded:: 1.5.10
save_backend: If ``save_images`` is :obj:`True`, the backend to use for
recording the images. It should be one of:
::
'sitk', 'cv2', 'pil', 'npy'
They correspond to the modules :mod:`SimpleITK`, :mod:`cv2` (OpenCV),
:mod:`PIL` (Pillow Fork), and :mod:`numpy`. Note that the ``'npy'``
backend saves the images as raw :obj:`numpy.array`, and thus ignores
the ``img_extension`` argument. Depending on the machine, some backends
may be faster or slower. For using each backend, the corresponding
Python must of course be installed. If not provided and ``save_images``
is :obj:`True`, the backends are tried in the same order as given above
and the first available one is used. ``'npy'`` is always available.
.. versionadded:: 1.5.10
image_generator: A callable taking two :obj:`float` as arguments and
returning an image as a :obj:`numpy.array`. **This argument is intended
for use in the examples of Crappy, to apply an artificial strain on a
base image. Most users should ignore it.** When given, the ``camera``
argument is ignored and the images are acquired from the generator. To
apply a strain on the image, strain values (in `%`) should be sent to
the Camera Block over the labels ``'Exx(%)'`` and ``'Eyy(%)'``.
.. versionadded:: 1.5.10
img_shape: The shape of the images returned by the
:class:`~crappy.camera.Camera` object as a :obj:`tuple` of :obj:`int`.
It should correspond to the value returned by :obj:`numpy.shape`.
**This argument is mandatory in case** ``config`` **is** :obj:`False`.
It is otherwise ignored.
.. versionadded:: 2.0.0
img_dtype: The `dtype` of the images returned by the
:class:`~crappy.camera.Camera` object, as a :obj:`str`. It should
correspond to a valid data type in :mod:`numpy`, e.g. ``'uint8'``.
**This argument is mandatory in case** ``config`` **is** :obj:`False`.
It is otherwise ignored.
.. versionadded:: 2.0.0
patches: The coordinates of the several patches to track, as an iterable
(like a :obj:`list` or a :obj:`tuple`) containing one or several
:obj:`tuple` of exactly :obj:`int` values. These integers correspond to
the `y` position of the top-left corner of the patch, the `x` position
of the top-left corner of the patch, the height of the patch, and the
width of the patch. Up to 4 patches can be given and tracked. This
argument must be provided if ``config`` is :obj:`False`.
labels: The labels to use for sending data to downstream Blocks. If not
given, the default labels are
``'t(s)', 'meta', 'Coord(px)', 'Eyy(%)', 'Exx(%)', 'Disp(px)'``. They
carry for each image its timestamp, a :obj:`dict` containing its
metadata, a :obj:`list` containing for each patch the coordinates of
its center in a :obj:`tuple` of :obj:`int`, the `y` and `x` strain
values calculated from the displacement and the initial position of the
patches, and finally a :obj:`list` containing for each patch its
displacement in the `y` and `x` direction in a :obj:`tuple` of
:obj:`int`. If different labels are desired, they should all be
provided at once in an iterable of :obj:`str` containing the correct
number of labels (6).
method: The method to use for performing the digital image correlation.
Should be one of :
::
`Disflow`, 'Pixel precision', 'Parabola', 'Lucas Kanade'
``'Disflow'`` uses OpenCV's DISOpticalFlow and ``'Lucas Kanade'`` uses
OpenCV's calcOpticalFlowPyrLK, while all other methods are based on a
basic cross-correlation in the Fourier domain. ``'Pixel precision'``
calculates the displacement by getting the position of the maximum of
the cross-correlation, and has thus a 1-pixel resolution. It is mainly
meant for debugging. ``'Parabola'`` refines the result of
``'Pixel precision'`` by interpolating the neighborhood of the maximum,
and has thus a sub-pixel resolution.
.. versionadded:: 1.5.9
alpha: Weight of the smoothness term in DISFlow, as a :obj:`float`.
Ignored if ``method`` is not ``'Disflow'``.
delta: Weight of the color constancy term in DISFlow, as a :obj:`float`.
Ignored if ``method`` is not ``'Disflow'``.
gamma: Weight of the gradient constancy term in DISFlow , as a
:obj:`float`. Ignored if ``method`` is not ``'Disflow'``.
finest_scale: Finest level of the Gaussian pyramid on which the flow is
computed in DISFlow, as an :obj:`int`. Zero level corresponds to the
original image resolution. The final flow is obtained by bilinear
upscaling. Ignored if ``method`` is not ``'Disflow'``.
iterations: The number of fixed point iterations of variational
refinement per scale in DISFlow, as an :obj:`int`. Set to zero to
disable variational refinement completely. Higher values will typically
result in more smooth and high-quality flow. Ignored if ``method`` is
not ``'Disflow'``.
gradient_iterations: The maximum number of gradient descent iterations in
the patch inverse search stage in DISFlow, as an :obj:`int`. Higher
values may improve the quality. Ignored if ``method`` is not
``'Disflow'``.
.. versionchanged:: 1.5.10
renamed from *gditerations* to *gradient_iterations*
patch_size: The size of an image patch for matching in DISFlow, in pixels
as an :obj:`int`. Ignored if ``method`` is not ``'Disflow'``.
patch_stride: The stride between two neighbor patches in DISFlow, in
pixels as an :obj:`int`. Must be less than the ``patch_size``. Lower
values correspond to higher flow quality. Ignored if ``method`` is not
``'Disflow'``.
border: The ratio of the patch that is kept for calculating the
displacement, if ``method`` is ``'Disflow'``. For example if a value
of `0.2` is given, only the center `80%` of the image is used for
calculating the average displacement, in both directions. Ignored if
``method`` is not ``'Disflow'``.
safe: If :obj:`True`, checks at each new image if the patches are not
exiting the frame. Otherwise, the patches might exit the image which
can lead to an unexpected behavior without raising an error.
.. versionadded:: 1.5.7
follow: If :obj:`True`, the position of each patch on the images is
adjusted at each new image based on the previous computed displacement
of this patch. If a displacement of 1 in the `x` direction was
calculated on the previous image, and the patch is located at position
`(x0, y0)`, the patch will be moved to position `(x0 + 1, y0)` for the
next image. It "follows" the texture to track. Recommended if the
expected displacement in pixels is big compared to the patch size. The
only downside is that the patches may exit the frame if something goes
wrong with the tracking.
.. versionadded:: 1.5.7
raise_on_patch_exit: If :obj:`True`, raises an exception when a tracked
patch exits the border of the image, which stops the entire test.
Otherwise, just logs a warning message and sleeps until the test is
stopped in another way.
.. versionadded:: 2.0.0
**kwargs: Any additional argument will be passed to the
:class:`~crappy.camera.Camera` object, and used as a kwarg to its
:meth:`~crappy.camera.Camera.open` method.
.. versionremoved:: 1.5.9 *fields* argument
.. versionremoved:: 2.0.0 *img_name* argument
"""
if not config and patches is None:
raise ValueError("If the config window is disabled, patches must be "
"provided !")
super().__init__(camera=camera,
transform=transform,
config=config,
display_images=display_images,
displayer_backend=displayer_backend,
displayer_framerate=displayer_framerate,
software_trig_label=software_trig_label,
display_freq=display_freq,
freq=freq,
debug=debug,
save_images=save_images,
img_extension=img_extension,
save_folder=save_folder,
save_period=save_period,
save_backend=save_backend,
image_generator=image_generator,
img_shape=img_shape,
img_dtype=img_dtype,
**kwargs)
# Forcing the labels into a list
if labels is None:
self.labels = ['t(s)', 'meta', 'Coord(px)', 'Eyy(%)',
'Exx(%)', 'Disp(px)']
elif isinstance(labels, str):
self.labels = [labels]
else:
self.labels = list(labels)
# Making sure a coherent number of labels and fields was given
if len(self.labels) != 6:
raise ValueError("The number of labels should be 6 !\n"
"Make sure that the time label was given")
self._patches: Optional[SpotsBoxes] = None
self._raise_on_exit = raise_on_patch_exit
self._patches_int = list(patches) if patches is not None else None
# These arguments are for the DICVEProcess
self._method = method
self._alpha = alpha
self._delta = delta
self._gamma = gamma
self._finest_scale = finest_scale
self._iterations = iterations
self._gradient_iterations = gradient_iterations
self._patch_size = patch_size
self._patch_stride = patch_stride
self._border = border
self._safe = safe
self._follow = follow
[docs]
def prepare(self) -> None:
"""This method mostly calls the :meth:`~crappy.blocks.Camera.prepare`
method of the parent class.
In addition to that it instantiates the
:class:`~crappy.blocks.camera_processes.DICVEProcess` object that performs
the image correlation and the tracking.
.. versionchanged:: 1.5.5 now accepting args and kwargs
.. versionchanged:: 1.5.10 not accepting arguments anymore
"""
# Instantiating the SpotsBoxes containing the patches to track
self._patches = SpotsBoxes()
if self._patches_int is not None:
self._patches.set_spots(self._patches_int)
self._patches.save_length()
# Instantiating the DICVEProcess
self.process_proc = DICVEProcess(
patches=self._patches,
method=self._method,
alpha=self._alpha,
delta=self._delta,
gamma=self._gamma,
finest_scale=self._finest_scale,
iterations=self._iterations,
gradient_iterations=self._gradient_iterations,
patch_size=self._patch_size,
patch_stride=self._patch_stride,
border=self._border,
safe=self._safe,
follow=self._follow,
raise_on_exit=self._raise_on_exit)
super().prepare()
def _configure(self) -> None:
"""This method should instantiate and start the
:class:`~crappy.tool.camera_config.DICVEConfig` window for configuring the
:class:`~crappy.camera.Camera` object.
It should also handle the case when an exception is raised in the
configuration window.
"""
config = None
# Instantiating and starting the configuration window
try:
config = DICVEConfig(self._camera, self._log_queue, self._log_level,
self.freq, self._patches)
config.main()
# If an exception is raised in the config window, closing it before raising
except (Exception,) as exc:
self._logger.exception("Caught exception in the configuration window !",
exc_info=exc)
if config is not None:
config.stop()
raise CameraConfigError
# Getting the image dtype and shape for setting the shared Array
if config.shape is not None:
self._img_shape = config.shape
if config.dtype is not None:
self._img_dtype = config.dtype