diff --git a/misc/Extract.py b/misc/Extract.py
new file mode 100644
index 0000000000000000000000000000000000000000..0eec8c6993ea5e9bcf80575556ec2ed61b2cb412
--- /dev/null
+++ b/misc/Extract.py
@@ -0,0 +1,325 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+GUI to select and deselect cells at extraction time.
+"""
+
+import sys
+import numpy as np
+from PyQt5.QtWidgets import (QApplication, QWidget, QPushButton,
+ QHBoxLayout, QVBoxLayout)
+
+from PIL import Image, ImageDraw
+
+
+#Import from matplotlib to use it to display the pictures and masks.
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+
+from matplotlib import cm
+from matplotlib.colors import LinearSegmentedColormap
+from matplotlib.figure import Figure
+
+
+class Extract(QWidget):
+
+
+ def __init__(self):
+ super(Extract, self).__init__()
+ image, mask = _test_data()
+ self.pc = PlotCanvas(image, mask)
+ self.init_UI()
+ self.exit_code = 0 # 0: Cancel, 1: Fluorescence, 2: Mask
+
+ def init_UI(self):
+ # Extract Buttons
+ self.extr_mask = _create_button("Extract Mask", self.do_extr_mask)
+ self.extr_fluo = _create_button("Extract Fluorescence", self.do_extr_fluo)
+ self.done = _create_button("Cancel", self.do_cancel)
+
+ extr_box = QVBoxLayout()
+ extr_box.addWidget(self.extr_mask)
+ extr_box.addWidget(self.extr_fluo)
+ extr_box.addWidget(self.done)
+
+ # Select Button
+ self.sel_mult = _create_button("Select Multiple", self.do_sel_mult)
+ self.sel_sngl = _create_button("Select Single", self.do_sel_sngl)
+ self.desel_mult = _create_button("Deselect Multiple", self.do_desel_mult)
+ self.desel_sngl = _create_button("Deselect Single", self.do_desel_sngl)
+
+ sel_box = QVBoxLayout()
+ sel_box.addWidget(self.sel_mult)
+ sel_box.addWidget(self.sel_sngl)
+ sel_box.addWidget(self.desel_mult)
+ sel_box.addWidget(self.desel_sngl)
+
+ # Button list
+ self.buttons = [self.extr_mask,
+ self.extr_fluo,
+ self.done,
+ self.sel_mult,
+ self.sel_sngl,
+ self.desel_mult,
+ self.desel_sngl]
+
+ # Buttons
+ buttons = QHBoxLayout()
+ buttons.addLayout(sel_box)
+ buttons.addStretch(.5)
+ buttons.addLayout(extr_box)
+
+ # Plot Canvas
+ full = QVBoxLayout()
+ full.addWidget(self.pc)
+ full.addStretch(.5)
+ full.addLayout(buttons)
+
+ self.setLayout(full)
+ self.setGeometry(300, 300, 600, 600)
+ self.setWindowTitle('Extracting')
+ self.show()
+
+ def do_extr_fluo(self):
+ self.exit_code = 1
+ self.cells = self.pc.sellist
+ self.close()
+
+ def do_cancel(self):
+ self.close()
+
+ def do_extr_mask(self):
+ self.exit_code = 2
+ self.cells = self.pc.sellist
+ self.close()
+
+ def do_sel_mult(self):
+ """Callback for selecting multiple"""
+ self.pc.storemouseclicks = []
+ def to_connect(e):
+ self.pc.multiple_click(e, self.do_sel_mult_process)
+ self.pc.connect_id = self.pc.mpl_connect(
+ 'button_press_event',
+ to_connect)
+ self.deactivate_all()
+
+ def do_sel_mult_process(self):
+ """Process selecting multiple"""
+ cells = self.cells_in_polygon()
+ self.pc.sellist = self.pc.sellist.union(cells)
+ self.disconnect()
+
+ def do_desel_mult(self):
+ self.pc.storemouseclicks = []
+ """Callback for deselecting multiple"""
+ def to_connect(e):
+ self.pc.multiple_click(e, self.do_desel_mult_process)
+ self.pc.connect_id = self.pc.mpl_connect(
+ 'button_press_event',
+ to_connect)
+ self.deactivate_all()
+
+ def do_desel_mult_process(self):
+ """Process deselect multiple"""
+ cells = self.cells_in_polygon()
+ self.pc.sellist = self.pc.sellist - cells
+ self.disconnect()
+
+ def cells_in_polygon(self):
+ """Extracts cells inside of polygon specified by pc.storemouseclicks"""
+ img = Image.new('L', (self.pc.mask.shape), 0)
+ ImageDraw.Draw(img).polygon(self.pc.storemouseclicks, outline=1, fill=1)
+ polygon = np.array(img).astype(bool)
+ return set(np.unique(self.pc.mask[polygon]))
+
+ def do_sel_sngl(self):
+ """Select single cell"""
+ def to_connect(e):
+ self.pc.single_click(e, self.do_sel_sngl_process)
+ self.pc.connect_id = self.pc.mpl_connect(
+ 'button_press_event',
+ to_connect)
+ self.deactivate_all()
+
+ def do_sel_sngl_process(self, x, y):
+ """Process selected cell"""
+ if x is not None:
+ cell = self.pc.mask[y,x]
+ self.pc.sellist.add(cell)
+ self.disconnect()
+
+ def do_desel_sngl(self):
+ """Deselect single cell"""
+ def to_connect(e):
+ self.pc.single_click(e, self.do_desel_sngl_process)
+ self.pc.connect_id = self.pc.mpl_connect(
+ 'button_press_event',
+ to_connect)
+ self.deactivate_all()
+
+ def do_desel_sngl_process(self, x, y):
+ """Process deselected cell"""
+ if x is not None:
+ cell = self.pc.mask[y,x]
+ self.pc.sellist.remove(cell)
+ self.disconnect()
+
+ def disconnect(self):
+ """Disconnects callback, updates plots, activates buttons"""
+ self.pc.update_plots()
+ self.pc.mpl_disconnect(self.pc.connect_id)
+ self.activate_all()
+
+ def deactivate_all(self):
+ for b in self.buttons:
+ b.setEnabled(False)
+
+ def activate_all(self):
+ for b in self.buttons:
+ b.setEnabled(True)
+
+
+class PlotCanvas(FigureCanvas):
+
+
+ def __init__(self, image, mask, parent=None, figsize=(5,4)):
+ """this class defines the canvas. It initializes a figure, which is then
+ used to plot our data using imshow.
+ """
+ fig = Figure()
+ self.ax = fig.add_subplot(111)
+ super(PlotCanvas, self).__init__(fig)
+ self.setParent(parent)
+
+ self.image = image
+ self.mask = mask
+ self.sellist = set(np.unique(mask)) # selected cells
+ self.vismask = mask.copy() # mask with only selected cells
+
+ self.ax_image, self.ax_mask = self.initialize_plots(image, mask, self.ax)
+ self.storemouseclicks = []
+ self.connect_id = None
+
+ def initialize_plots(self, picture, mask, ax):
+ """Creates plots at initialization"""
+ newcmp = _colormap(21)
+ ax.axis("off")
+ self.draw()
+ return (ax.imshow(picture, interpolation= 'None',
+ origin = 'upper', cmap = 'gray_r'),
+ ax.imshow((mask%10+1)*(mask != 0), origin = 'upper',
+ interpolation = 'None', cmap = newcmp,
+ vmin=0, vmax=11))
+
+ def single_click(self, event, call_after):
+ """Function for single click, calls call_after afterwards with
+ the clicked points (or None, None) if abort click."""
+ if (event.button == 1
+ and (event.xdata != None and event.ydata != None)
+ and self.ax == event.inaxes):
+ x = int(event.xdata)
+ y = int(event.ydata)
+ call_after(x, y)
+ else:
+ call_after(None, None)
+
+ def multiple_click(self, event, call_after):
+ """Function to keep track of multiple left clicks, confirmed with
+ a right click. After right click, the function call_after is called"""
+
+ if (event.button == 1 # left click
+ and (event.xdata != None and event.ydata != None)
+ and self.ax == event.inaxes):
+
+ newx = int(event.xdata)
+ newy = int(event.ydata)
+ self.storemouseclicks.append((newx, newy))
+ self.draw_click(newx, newy)
+
+ elif (event.button == 3): # right click
+ self.mpl_disconnect(self.connect_id)
+ call_after()
+
+ def draw_click(self, posx, posy):
+ """
+ it updates the plot once the user clicks on the plot and draws a 4x4 pixel dot
+ at the coordinate of the click
+ """
+ self.vismask[posy:posy+2, posx:posx+2] = 9
+ self.redraw_mask()
+
+ def redraw_mask(self):
+ """Redraw mask with current self.vismask"""
+ self.ax_mask.set_data((self.vismask%10+1)*(self.vismask!=0))
+ self.ax.draw_artist(self.ax_image)
+ self.ax.draw_artist(self.ax_mask)
+ self.update()
+ self.flush_events()
+
+ def recalculate_vismask(self):
+ """Recalculates vismask with current list of cells to show"""
+ tmp = self.mask.copy()
+ all_cells = set(np.unique(tmp))
+ to_remove = all_cells - self.sellist
+ for cell in to_remove:
+ tmp[tmp==cell] = 0
+ self.vismask = tmp
+
+ def update_plots(self):
+ """Shows plot with currently selected cells"""
+ self.recalculate_vismask()
+ self.redraw_mask()
+
+def _create_button(text, connect, tooltip=None):
+ """Initializes button, connects with callback connect"""
+ button = QPushButton(text)
+ button.clicked.connect(connect)
+ button.setMaximumWidth(150)
+
+ if tooltip is not None:
+ button.setToolTip(tooltip)
+
+ return button
+
+def _colormap(Ncolors=21):
+ """Creates colormap for segmentation mask"""
+ jet = cm.get_cmap('jet', Ncolors)
+
+ cmaplist = [(0,0,0,0)]
+ for i in range(jet.N):
+ r,g,b,_ = jet(i)
+ cmaplist.append((r,g,b,.2))
+ cmap = LinearSegmentedColormap.from_list('Custom cmap', cmaplist, Ncolors)
+ return cmap
+
+def _poly_to_mask(polygon, shape):
+ """Converts polygon to mask"""
+ img = Image.new('L', shape, 0)
+ ImageDraw.Draw(img).polygon(polygon, outline=0, fill=1)
+ return np.array(img).astype(int)
+
+def _poly_to_line(polygon, shape):
+ """Converts polygon to line"""
+ img = Image.new('L', shape, 0)
+ ImageDraw.Draw(img).polygon(polygon, outline=1, fill=0)
+ return np.array(img).astype(int)
+
+def _test_data():
+ """Creates test data"""
+ im = np.zeros((100,100))
+ mask = np.zeros(im.shape)
+
+ poly1 = [(20,20),(30,30),(20,40),(10,30)]
+ poly2 = [(50,50),(60,60),(50,70),(40,60)]
+
+ mask += _poly_to_mask(poly1, im.shape)
+ mask += _poly_to_mask(poly2, im.shape)*2
+ im += _poly_to_line(poly1, im.shape)
+ im += _poly_to_line(poly2, im.shape)
+
+ return im, mask
+
+
+if __name__ == '__main__':
+ app = QApplication(sys.argv)
+ ex = Extract()
+ sys.exit(app.exec_())
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