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feat: version 3.3.0
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@@ -65,3 +65,8 @@ _docs | |
| docs/tested_blocks.md | ||
| docs/md/all_blocks.rst | ||
| docs/md/template.py | ||
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| ## Pycharm | ||
| *.xml | ||
| .idea | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,145 +1,163 @@ | ||
| import io | ||
| import shutil | ||
| import tempfile | ||
| import time | ||
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| import imageio | ||
| import matplotlib.pyplot as plt | ||
| import numpy as np | ||
| from matplotlib.backends.backend_agg import FigureCanvasAgg | ||
| from skimage.transform import resize | ||
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| from prose import Block, viz | ||
| from prose.visualization import corner_text | ||
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| __all__ = ["VideoPlot"] | ||
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| def im_to_255(image, factor=0.25): | ||
| if factor != 1: | ||
| return ( | ||
| resize( | ||
| image.astype(float), | ||
| (np.array(np.shape(image)) * factor).astype(int), | ||
| anti_aliasing=False, | ||
| ) | ||
| * 255 | ||
| ).astype("uint8") | ||
| else: | ||
| data = image.copy().astype(float) | ||
| data = data / np.max(data) | ||
| data = data * 255 | ||
| return data.astype("uint8") | ||
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| class _Video(Block): | ||
| """Base block to build a video""" | ||
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| def __init__(self, destination, fps=10, **kwargs): | ||
| super().__init__(**kwargs) | ||
| self.destination = destination | ||
| self.images = [] | ||
| self.fps = fps | ||
| self.checked_writer = False | ||
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| def run(self, image): | ||
| if not self.checked_writer: | ||
| _ = imageio.get_writer(self.destination, mode="I") | ||
| self.checked_writer = True | ||
| from prose.core.block import Block | ||
| from prose.utils import z_scale | ||
|
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| def terminate(self): | ||
| imageio.mimsave(self.destination, self.images, fps=self.fps) | ||
| __all__ = ["VideoPlot", "Video"] | ||
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| @property | ||
| def citations(self): | ||
| return super().citations + ["imageio"] | ||
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| def im_to_255(image): | ||
| data = image.copy().astype(float) | ||
| data = data / np.max(data) | ||
| data = data * 255 | ||
| return data.astype("uint8") | ||
|
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| class RawVideo(_Video): | ||
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| class Video(Block): | ||
| def __init__( | ||
| self, destination, attribute="data", fps=10, function=None, scale=1, **kwargs | ||
| self, | ||
| destination, | ||
| fps=10, | ||
| compression=None, | ||
| data_function=None, | ||
| width=None, | ||
| contrast=0.1, | ||
| name=None, | ||
| ): | ||
| super().__init__(destination, fps=fps, **kwargs) | ||
| if function is None: | ||
| """ | ||
| A block to create a video from images data (using ffmpeg). | ||
| def _donothing(data): | ||
| return data | ||
| Parameters | ||
| ---------- | ||
| destination : str | ||
| The path to save the resulting video. | ||
| fps : int, optional | ||
| The frames per second of the resulting video. Default is 10. | ||
| compression : int, optional | ||
| The compression rate of the resulting video (-cr value of fmmpeg). | ||
| Default is None. | ||
| data_function : callable, optional | ||
| A function to apply to each image data before adding it to the video. | ||
| If none, a z scale is applied to the data with a contrast given by | ||
| :code:`contrast`.Default is None. | ||
| width : int, optional | ||
| The width in pixels of the resulting video. | ||
| Default is None (i.e. original image size). | ||
| contrast : float, optional | ||
| The contrast of the resulting video. Default is 0.1. | ||
| Either :code:`contrast` or :code:`data_function` must be provided. | ||
| name : str, optional | ||
| The name of the block. Default is None. | ||
| Attributes | ||
| ---------- | ||
| citations : list of str | ||
| The citations for the block. | ||
| function = _donothing | ||
| Methods | ||
| ------- | ||
| run(image) | ||
| Adds an image to the video. | ||
| terminate() | ||
| Closes the video writer. | ||
| self.function = function | ||
| self.scale = scale | ||
| self.attribute = attribute | ||
| """ | ||
| super().__init__(name=name) | ||
| if data_function is None: | ||
|
|
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| def data_function(data): | ||
| new_data = data.copy() | ||
| new_data = z_scale(new_data, c=contrast) | ||
| return new_data | ||
|
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| output = [] | ||
| if compression is not None: | ||
| output += ["-crf", f"{compression}"] | ||
| if width is not None: | ||
| output += ["-vf", f"scale={width}:-1"] | ||
| self.writer = imageio.get_writer( | ||
| destination, | ||
| mode="I", | ||
| fps=fps, | ||
| output_params=output if len(output) > 0 else None, | ||
| ) | ||
| self.function = data_function | ||
|
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| def run(self, image): | ||
| super().run(image) | ||
| data = self.function(image.__dict__[self.attribute]) | ||
| self.images.append(im_to_255(data, factor=self.scale)) | ||
| data = self.function(image.data) | ||
| self.writer.append_data(im_to_255(data)) | ||
|
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| def terminate(self): | ||
| self.writer.close() | ||
|
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| @property | ||
| def citations(self): | ||
| return super().citations + ["imageio"] | ||
|
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| class VideoPlot(_Video): | ||
| def __init__(self, plot_function, destination, fps=10, name=None): | ||
| """Make a video out of a plotting function | ||
|
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| class VideoPlot(Video): | ||
| def __init__( | ||
| self, | ||
| plot_function, | ||
| destination, | ||
| fps=10, | ||
| compression=None, | ||
| width=None, | ||
| name=None, | ||
| ): | ||
| """ | ||
| A block to create a video from a matploltib plot (using ffmpeg). | ||
| Parameters | ||
| ---------- | ||
| plot_function : function | ||
| a plotting function taking an :py:class:`prose.Image` as input | ||
| destination : str or Path | ||
| destination of the video, including extension | ||
| plot_function : callable | ||
| A function that takes an image as input and produce a plot. | ||
| destination : str | ||
| The path to save the resulting video. | ||
| fps : int, optional | ||
| frame per seconds, by default 10 | ||
| antialias : bool, optional | ||
| whether pyplot antialias should be used, by default False | ||
| The frames per second of the resulting video. Default is 10. | ||
| compression : int, optional | ||
| The compression rate of the resulting video (-cr value of fmmpeg). | ||
| Default is None. | ||
| width : int, optional | ||
| The width in pixels of the resulting video. | ||
| Default is None (i.e. original image size). | ||
| name : str, optional | ||
| The name of the block. Default is None. | ||
| Attributes | ||
| ---------- | ||
| citations : list of str | ||
| The citations for the block. | ||
| Methods | ||
| ------- | ||
| run(image) | ||
| Adds a plot to the video. | ||
| terminate() | ||
| Closes the video writer. | ||
| """ | ||
| super().__init__(destination, fps=fps, name=name) | ||
| super().__init__( | ||
| destination, | ||
| fps=fps, | ||
| compression=compression, | ||
| width=width, | ||
| name=name, | ||
| ) | ||
| self.plot_function = plot_function | ||
| self.destination = destination | ||
| self._temp = tempfile.mkdtemp() | ||
| self._images = [] | ||
|
|
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| def run(self, image): | ||
| self.plot_function(image) | ||
| buf = io.BytesIO() | ||
| plt.savefig(buf) | ||
| self.images.append(imageio.imread(buf)) | ||
| self.writer.append_data(imageio.imread(buf)) | ||
| plt.close() | ||
|
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| def terminate(self): | ||
| super().terminate() | ||
| shutil.rmtree(self._temp) | ||
|
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|
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| class LivePlot(Block): | ||
| def __init__(self, plot_function=None, sleep=0.0, size=None, **kwargs): | ||
| super().__init__(**kwargs) | ||
| if plot_function is None: | ||
| plot_function = lambda im: viz.show_stars( | ||
| im.data, | ||
| im.stars_coords if hasattr(im, "stars_coords") else None, | ||
| size=size, | ||
| ) | ||
|
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| self.plot_function = plot_function | ||
| self.sleep = sleep | ||
| self.display = None | ||
| self.size = size | ||
| self.figure_added = False | ||
|
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| def run(self, image): | ||
| if not self.figure_added: | ||
| from IPython import display as disp | ||
|
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| self.display = disp | ||
| if isinstance(self.size, tuple): | ||
| plt.figure(figsize=self.size) | ||
| self.figure_added = True | ||
|
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| self.plot_function(image) | ||
| self.display.clear_output(wait=True) | ||
| self.display.display(plt.gcf()) | ||
| time.sleep(self.sleep) | ||
| plt.cla() | ||
|
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| def terminate(self): | ||
| plt.close() | ||
| super().terminate() |
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