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C-AchardC-Achard
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split plugins in separate scripts
1 parent af64848 commit 3e7c432

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3 files changed

+206
-5
lines changed

3 files changed

+206
-5
lines changed

‎napari_cellseg_annotator/plugin_helper.py‎

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import napari
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from qtpy.QtWidgets import QWidget, QVBoxLayout, QPushButton
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from napari_cellseg_annotator import utils
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class Helper(QWidget):
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# widget testing
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def __init__(self, parent: "napari.viewer.Viewer"):
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super().__init__()
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# self.master = parent
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self.help_url = "https://github.com/C-Achard/cellseg-annotator-test/tree/main"
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self.about_url = (
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"https://wysscenter.ch/advances/3d-computer-vision-for-brain-analysis"
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)
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self._viewer = parent
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self.btn1 = QPushButton("Help...", self)
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# self.btn1.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btn1.clicked.connect(lambda: utils.open_url(self.help_url))
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self.btn2 = QPushButton("About...", self)
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# self.btn2.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btn2.clicked.connect(lambda: utils.open_url(self.about_url))
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self.btnc = QPushButton("Close", self)
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# self.btnc.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btnc.clicked.connect(self.close)
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self.build()
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def build(self):
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vbox = QVBoxLayout()
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vbox.addWidget(self.btn1)
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vbox.addWidget(self.btn2)
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vbox.addWidget(self.btnc)
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self.setLayout(vbox)
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self.show()
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def close(self):
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self._viewer.window.remove_dock_widget(self)
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‎napari_cellseg_annotator/plugin_loader.py‎

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import os
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from pathlib import Path
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import napari
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import numpy as np
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from qtpy.QtWidgets import (
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QWidget,
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QVBoxLayout,
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QPushButton,
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QSizePolicy,
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QLabel,
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QFileDialog,
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QLineEdit,
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QCheckBox,
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)
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from skimage import io
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from napari_cellseg_annotator import utils
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from napari_cellseg_annotator.napari_view_simple import launch_viewers
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def format_Warning(message, category, filename, lineno, line=""):
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return (
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str(filename)
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+ ":"
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+ str(lineno)
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+ ": "
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+ category.__name__
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+ ": "
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+ str(message)
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+ "\n"
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)
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warnings.formatwarning = format_Warning
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class Loader(QWidget):
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def __init__(self, parent: "napari.viewer.Viewer"):
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super().__init__()
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# self.master = parent
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self._viewer = parent
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self.opath = ""
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self.modpath = ""
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self.btn1 = QPushButton("Open", self)
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self.btn1.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btn1.clicked.connect(self.show_dialog_o)
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self.btn2 = QPushButton("Open", self)
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self.btn2.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btn2.clicked.connect(self.show_dialog_mod)
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self.textbox = QLineEdit(self)
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self.textbox.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.checkBox = QCheckBox("Create new dataset?")
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self.checkBox.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btn4 = QPushButton("Start reviewing", self)
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self.btn4.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btn4.clicked.connect(self.launch_napari)
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self.btn4.clicked.connect(self.close)
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self.btnb = QPushButton("Close", self)
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self.btnb.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btnb.clicked.connect(self.close)
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self.lbl = QLabel("Images directory", self)
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self.lbl2 = QLabel("Labels directory", self)
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self.lbl4 = QLabel("Model name", self)
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#####################################################################
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# TODO
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self.btntest = QPushButton("test", self)
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self.btntest.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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self.btntest.clicked.connect(self.run_test)
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#####################################################################
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self.build()
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def build(self):
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vbox = QVBoxLayout()
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vbox.addWidget(utils.combine_blocks(self.btn1, self.lbl))
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vbox.addWidget(utils.combine_blocks(self.btn2, self.lbl2))
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vbox.addWidget(utils.combine_blocks(self.textbox, self.lbl4))
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vbox.addWidget(self.checkBox)
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vbox.addWidget(self.btn4)
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vbox.addWidget(self.btnb)
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##################################################################
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# TODO : remove once done
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test = True
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if test:
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vbox.addWidget(self.btntest)
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##################################################################
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self.setLayout(vbox)
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self.show()
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def show_dialog_o(self):
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default_path = max(self.opath, self.modpath, os.path.expanduser("~"))
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f_name = QFileDialog.getExistingDirectory(self, "Open directory", default_path)
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if f_name:
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self.opath = f_name
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self.lbl.setText(self.opath)
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def show_dialog_mod(self):
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default_path = max(self.opath, self.modpath, os.path.expanduser("~"))
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f_name = QFileDialog.getExistingDirectory(self, "Open directory", default_path)
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if f_name:
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self.modpath = f_name
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self.lbl2.setText(self.modpath)
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def close(self):
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# self.master.setCurrentIndex(0)
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self._viewer.window.remove_dock_widget(self)
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def launch_napari(self):
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images = utils.load_images(self.opath)
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if self.modpath == "": # saves empty images of the same size as original images
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labels = np.zeros_like(images.compute()) # dask to numpy
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self.modpath = os.path.join(
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os.path.dirname(self.opath), self.textbox.text()
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)
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os.makedirs(self.modpath, exist_ok=True)
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filenames = [
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fn.name for fn in sorted(list(Path(self.opath).glob("./*png")))
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]
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for i in range(len(labels)):
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io.imsave(
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os.path.join(self.modpath, str(i).zfill(4) + ".png"), labels[i]
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)
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else:
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labels = utils.load_saved_masks(self.modpath)
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try:
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labels_raw = utils.load_raw_masks(self.modpath + "_raw")
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except:
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labels_raw = None
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# TODO: viewer argument ?
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view1 = launch_viewers(
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self._viewer,
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images,
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labels,
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labels_raw,
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self.modpath,
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self.textbox.text(),
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self.checkBox.isChecked(),
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)
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# global view_l
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# view_l.close() # why does it not close the window ?? #TODO use self.close() ?
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# self.close
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return view1
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########################
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# TODO : remove once done
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def run_test(self):
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tif = False
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self.opath = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_png/sample"
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self.modpath = (
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"C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_png/sample_labels"
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)
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if tif:
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self.opath = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_tif/volumes"
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self.modpath = "C:/Users/Cyril/Desktop/Proj_bachelor/data/visual_tif/labels"
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self.launch_napari()
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self.close()
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########################

‎napari_cellseg_annotator/plugins.py‎

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Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
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from napari_cellseg_annotator.annotator import Loader, Helper
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from napari_cellseg_annotator.plugin_helper import Helper
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from napari_cellseg_annotator.plugin_loader import Loader
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def napari_experimental_provide_dock_widget():
5-
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return [
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(Loader, {"name": "File loader"}),
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(Trainer, {"name": "Trainer"}),
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(Predicter, {"name": "Predicter"}),
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(Helper, {"name": "Help/About..."}),
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# (Trainer, {"name": "Trainer"}),
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# (Predicter, {"name": "Predicter"}),
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]
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