Fixed database typo and removed unnecessary class identifier.
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parent
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5098 changed files with 952558 additions and 85 deletions
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from .core import ImageViewer, CollectionViewer
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395
venv/Lib/site-packages/skimage/viewer/viewers/core.py
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395
venv/Lib/site-packages/skimage/viewer/viewers/core.py
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"""
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ImageViewer class for viewing and interacting with images.
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"""
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import numpy as np
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from ... import io, img_as_float
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from ...util.dtype import dtype_range
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from ...exposure import rescale_intensity
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from ..qt import QtWidgets, QtGui, Qt, Signal
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from ..widgets import Slider
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from ..utils import (dialogs, init_qtapp, figimage, start_qtapp,
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update_axes_image)
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from ..utils.canvas import BlitManager, EventManager
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from ..plugins.base import Plugin
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__all__ = ['ImageViewer', 'CollectionViewer']
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def mpl_image_to_rgba(mpl_image):
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"""Return RGB image from the given matplotlib image object.
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Each image in a matplotlib figure has its own colormap and normalization
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function. Return RGBA (RGB + alpha channel) image with float dtype.
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Parameters
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----------
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mpl_image : matplotlib.image.AxesImage object
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The image being converted.
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Returns
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-------
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img : array of float, shape (M, N, 4)
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An image of float values in [0, 1].
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"""
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image = mpl_image.get_array()
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if image.ndim == 2:
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input_range = (mpl_image.norm.vmin, mpl_image.norm.vmax)
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image = rescale_intensity(image, in_range=input_range)
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# cmap complains on bool arrays
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image = mpl_image.cmap(img_as_float(image))
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elif image.ndim == 3 and image.shape[2] == 3:
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# add alpha channel if it's missing
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image = np.dstack((image, np.ones_like(image)))
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return img_as_float(image)
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class ImageViewer(QtWidgets.QMainWindow):
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"""Viewer for displaying images.
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This viewer is a simple container object that holds a Matplotlib axes
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for showing images. `ImageViewer` doesn't subclass the Matplotlib axes (or
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figure) because of the high probability of name collisions.
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Subclasses and plugins will likely extend the `update_image` method to add
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custom overlays or filter the displayed image.
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Parameters
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----------
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image : array
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Image being viewed.
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Attributes
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----------
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canvas, fig, ax : Matplotlib canvas, figure, and axes
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Matplotlib canvas, figure, and axes used to display image.
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image : array
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Image being viewed. Setting this value will update the displayed frame.
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original_image : array
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Plugins typically operate on (but don't change) the *original* image.
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plugins : list
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List of attached plugins.
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Examples
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--------
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>>> from skimage import data
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>>> image = data.coins()
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>>> viewer = ImageViewer(image) # doctest: +SKIP
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>>> viewer.show() # doctest: +SKIP
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"""
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dock_areas = {'top': Qt.TopDockWidgetArea,
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'bottom': Qt.BottomDockWidgetArea,
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'left': Qt.LeftDockWidgetArea,
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'right': Qt.RightDockWidgetArea}
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# Signal that the original image has been changed
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original_image_changed = Signal(np.ndarray)
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def __init__(self, image, useblit=True):
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# Start main loop
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init_qtapp()
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super(ImageViewer, self).__init__()
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# TODO: Add ImageViewer to skimage.io window manager
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self.setAttribute(Qt.WA_DeleteOnClose)
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self.setWindowTitle("Image Viewer")
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self.file_menu = QtWidgets.QMenu('&File', self)
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self.file_menu.addAction('Open file', self.open_file,
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Qt.CTRL + Qt.Key_O)
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self.file_menu.addAction('Save to file', self.save_to_file,
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Qt.CTRL + Qt.Key_S)
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self.file_menu.addAction('Quit', self.close,
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Qt.CTRL + Qt.Key_Q)
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self.menuBar().addMenu(self.file_menu)
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self.main_widget = QtWidgets.QWidget()
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self.setCentralWidget(self.main_widget)
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if isinstance(image, Plugin):
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plugin = image
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image = plugin.filtered_image
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plugin.image_changed.connect(self._update_original_image)
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# When plugin is started, start
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plugin._started.connect(self._show)
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self.fig, self.ax = figimage(image)
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self.canvas = self.fig.canvas
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self.canvas.setParent(self)
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self.ax.autoscale(enable=False)
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self._tools = []
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self.useblit = useblit
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if useblit:
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self._blit_manager = BlitManager(self.ax)
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self._event_manager = EventManager(self.ax)
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self._image_plot = self.ax.images[0]
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self._update_original_image(image)
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self.plugins = []
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self.layout = QtWidgets.QVBoxLayout(self.main_widget)
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self.layout.addWidget(self.canvas)
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status_bar = self.statusBar()
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self.status_message = status_bar.showMessage
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sb_size = status_bar.sizeHint()
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cs_size = self.canvas.sizeHint()
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self.resize(cs_size.width(), cs_size.height() + sb_size.height())
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self.connect_event('motion_notify_event', self._update_status_bar)
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def __add__(self, plugin):
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"""Add plugin to ImageViewer"""
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plugin.attach(self)
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self.original_image_changed.connect(plugin._update_original_image)
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if plugin.dock:
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location = self.dock_areas[plugin.dock]
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dock_location = Qt.DockWidgetArea(location)
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dock = QtWidgets.QDockWidget()
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dock.setWidget(plugin)
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dock.setWindowTitle(plugin.name)
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self.addDockWidget(dock_location, dock)
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horiz = (self.dock_areas['left'], self.dock_areas['right'])
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dimension = 'width' if location in horiz else 'height'
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self._add_widget_size(plugin, dimension=dimension)
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return self
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def _add_widget_size(self, widget, dimension='width'):
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widget_size = widget.sizeHint()
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viewer_size = self.frameGeometry()
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dx = dy = 0
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if dimension == 'width':
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dx = widget_size.width()
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elif dimension == 'height':
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dy = widget_size.height()
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w = viewer_size.width()
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h = viewer_size.height()
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self.resize(w + dx, h + dy)
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def open_file(self, filename=None):
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"""Open image file and display in viewer."""
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if filename is None:
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filename = dialogs.open_file_dialog()
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if filename is None:
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return
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image = io.imread(filename)
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self._update_original_image(image)
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def update_image(self, image):
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"""Update displayed image.
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This method can be overridden or extended in subclasses and plugins to
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react to image changes.
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"""
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self._update_original_image(image)
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def _update_original_image(self, image):
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self.original_image = image # update saved image
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self.image = image.copy() # update displayed image
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self.original_image_changed.emit(image)
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def save_to_file(self, filename=None):
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"""Save current image to file.
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The current behavior is not ideal: It saves the image displayed on
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screen, so all images will be converted to RGB, and the image size is
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not preserved (resizing the viewer window will alter the size of the
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saved image).
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"""
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if filename is None:
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filename = dialogs.save_file_dialog()
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if filename is None:
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return
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if len(self.ax.images) == 1:
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io.imsave(filename, self.image)
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else:
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underlay = mpl_image_to_rgba(self.ax.images[0])
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overlay = mpl_image_to_rgba(self.ax.images[1])
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alpha = overlay[:, :, 3]
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# alpha can be set by channel of array or by a scalar value.
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# Prefer the alpha channel, but fall back to scalar value.
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if np.all(alpha == 1):
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alpha = np.ones_like(alpha) * self.ax.images[1].get_alpha()
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alpha = alpha[:, :, np.newaxis]
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composite = (overlay[:, :, :3] * alpha +
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underlay[:, :, :3] * (1 - alpha))
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io.imsave(filename, composite)
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def closeEvent(self, event):
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self.close()
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def _show(self, x=0):
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self.move(x, 0)
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for p in self.plugins:
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p.show()
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super(ImageViewer, self).show()
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self.activateWindow()
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self.raise_()
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def show(self, main_window=True):
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"""Show ImageViewer and attached plugins.
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This behaves much like `matplotlib.pyplot.show` and `QWidget.show`.
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"""
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self._show()
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if main_window:
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start_qtapp()
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return [p.output() for p in self.plugins]
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def redraw(self):
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if self.useblit:
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self._blit_manager.redraw()
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else:
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self.canvas.draw_idle()
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@property
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def image(self):
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return self._img
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@image.setter
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def image(self, image):
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self._img = image
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update_axes_image(self._image_plot, image)
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# update display (otherwise image doesn't fill the canvas)
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h, w = image.shape[:2]
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self.ax.set_xlim(0, w)
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self.ax.set_ylim(h, 0)
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# update color range
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clim = dtype_range[image.dtype.type]
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if clim[0] < 0 and image.min() >= 0:
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clim = (0, clim[1])
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self._image_plot.set_clim(clim)
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if self.useblit:
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self._blit_manager.background = None
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self.redraw()
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def reset_image(self):
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self.image = self.original_image.copy()
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def connect_event(self, event, callback):
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"""Connect callback function to matplotlib event and return id."""
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cid = self.canvas.mpl_connect(event, callback)
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return cid
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def disconnect_event(self, callback_id):
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"""Disconnect callback by its id (returned by `connect_event`)."""
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self.canvas.mpl_disconnect(callback_id)
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def _update_status_bar(self, event):
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if event.inaxes and event.inaxes.get_navigate():
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self.status_message(self._format_coord(event.xdata, event.ydata))
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else:
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self.status_message('')
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def add_tool(self, tool):
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if self.useblit:
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self._blit_manager.add_artists(tool.artists)
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self._tools.append(tool)
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self._event_manager.attach(tool)
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def remove_tool(self, tool):
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if tool not in self._tools:
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return
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if self.useblit:
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self._blit_manager.remove_artists(tool.artists)
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self._tools.remove(tool)
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self._event_manager.detach(tool)
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def _format_coord(self, x, y):
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# callback function to format coordinate display in status bar
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x = int(x + 0.5)
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y = int(y + 0.5)
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try:
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return "%4s @ [%4s, %4s]" % (self.image[y, x], x, y)
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except IndexError:
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return ""
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class CollectionViewer(ImageViewer):
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"""Viewer for displaying image collections.
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Select the displayed frame of the image collection using the slider or
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with the following keyboard shortcuts:
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left/right arrows
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Previous/next image in collection.
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number keys, 0--9
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0% to 90% of collection. For example, "5" goes to the image in the
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middle (i.e. 50%) of the collection.
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home/end keys
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First/last image in collection.
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Parameters
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----------
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image_collection : list of images
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List of images to be displayed.
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update_on : {'move' | 'release'}
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Control whether image is updated on slide or release of the image
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slider. Using 'on_release' will give smoother behavior when displaying
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large images or when writing a plugin/subclass that requires heavy
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computation.
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"""
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def __init__(self, image_collection, update_on='move', **kwargs):
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self.image_collection = image_collection
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self.index = 0
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self.num_images = len(self.image_collection)
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first_image = image_collection[0]
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super(CollectionViewer, self).__init__(first_image)
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slider_kws = dict(value=0, low=0, high=self.num_images - 1)
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slider_kws['update_on'] = update_on
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slider_kws['callback'] = self.update_index
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slider_kws['value_type'] = 'int'
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self.slider = Slider('frame', **slider_kws)
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self.layout.addWidget(self.slider)
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# TODO: Adjust height to accommodate slider; the following doesn't work
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# s_size = self.slider.sizeHint()
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# cs_size = self.canvas.sizeHint()
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# self.resize(cs_size.width(), cs_size.height() + s_size.height())
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def update_index(self, name, index):
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"""Select image on display using index into image collection."""
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index = int(round(index))
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if index == self.index:
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return
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# clip index value to collection limits
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index = max(index, 0)
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index = min(index, self.num_images - 1)
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self.index = index
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self.slider.val = index
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self.update_image(self.image_collection[index])
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def keyPressEvent(self, event):
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if type(event) == QtGui.QKeyEvent:
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key = event.key()
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# Number keys (code: 0 = key 48, 9 = key 57) move to deciles
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if 48 <= key < 58:
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index = int(0.1 * (key - 48) * self.num_images)
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self.update_index('', index)
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event.accept()
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else:
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event.ignore()
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else:
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event.ignore()
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