def __init__(self, parent, viewer_reference):
QtWidgets.QDockWidget.__init__(self, parent)
self.setFloating(True)
self.setWindowTitle('Caiman detrend ΔF/F')
self.vi = ViewerUtils(viewer_reference)
opts = \
{
'quantileMin':
{
'minmax': (0, 100)
},
'frames_window':
{
'minmax': (0, 1000),
'step': 10
}
}
self.function = Function(detrend_df_f, opts, parent=self)
self.function.sig_set_clicked.connect(self.set_data)
self.setWidget(self.function.widget)
class NusetWidget(QtWidgets.QWidget):
sig_zlevel_changed = QtCore.pyqtSignal(int)
def __init__(self, parent, viewer_ref):
QtWidgets.QWidget.__init__(self, parent)
self.vlayout = QtWidgets.QVBoxLayout(self)
self.splitter = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
self.vlayout.addWidget(self.splitter)
self.left_layout = QtWidgets.QVBoxLayout(self)
self.left_widget = QtWidgets.QWidget(self.splitter)
self.left_widget.setLayout(self.left_layout)
hlayout_custom_img = QtWidgets.QHBoxLayout(self.left_widget)
self.lineedit_custom_img_path = QtWidgets.QLineEdit(self.left_widget)
self.lineedit_custom_img_path.setPlaceholderText(
"Path to custom image or stack")
self.lineedit_custom_img_path.setToolTip(
"Use a different image or stack for segmentation, such as an image or stack of nuclei."
)
self.button_use_custom = QtWidgets.QPushButton(self.left_widget)
self.button_use_custom.setMaximumWidth(50)
self.button_use_custom.setText("Set")
hlayout_custom_img.addWidget(self.lineedit_custom_img_path)
hlayout_custom_img.addWidget(self.button_use_custom)
self.left_layout.addLayout(hlayout_custom_img)
hlayout_projection_radios = QtWidgets.QHBoxLayout(self.left_widget)
self.radio_std = QtWidgets.QRadioButton(self.left_widget)
self.radio_std.setText("Std. Deviation")
self.radio_max = QtWidgets.QRadioButton(self.left_widget)
self.radio_max.setText("Max")
self.radio_mean = QtWidgets.QRadioButton(self.left_widget)
self.radio_mean.setText("Mean")
self.projection_option: str = ''
for w in [self.radio_std, self.radio_max, self.radio_mean]:
hlayout_projection_radios.addWidget(w)
w.clicked.connect(self.update_projection)
label_projections = QtWidgets.QLabel(self.left_widget)
label_projections.setText("Choose Input Projection")
label_projections.setStyleSheet("font-weight: bold")
self.left_layout.addWidget(label_projections)
self.left_layout.addLayout(hlayout_projection_radios)
# projection image
self.glw_raw = GraphicsLayoutWidget(self.left_widget)
self.imgitem_raw = ImageItem()
self.viewbox_raw = self.glw_raw.addViewBox()
self.viewbox_raw.setAspectLocked(True)
self.viewbox_raw.addItem(self.imgitem_raw)
self.left_layout.addWidget(self.glw_raw)
hlayout_preprocess = QtWidgets.QHBoxLayout(self.left_widget)
arg_opts_preprocess = \
{
'img': {'ignore': True},
'sigmoid_cutoff': {
'step': 10,
'minmax': (0, 9999.9)
},
'sigmoid_gain': {
'step': 0.01
},
'equalize_lower': {
'step': 0.01,
'minmax': (-1.0, 1.0)
},
'equalize_upper': {
'step': 0.01,
'minmax': (-1.0, 1.0)
}
}
self.preprocess_controls = \
Function(
get_preprocess,
arg_opts=arg_opts_preprocess,
parent=self.left_widget
)
self.preprocess_controls.button_set.hide()
self.preprocess_controls.sig_changed.connect(self.update_preprocess)
self.preprocess_controls.set_title("Pre-process Settings")
hlayout_preprocess.addWidget(self.preprocess_controls.widget)
self.zslider = QtWidgets.QSlider(parent=self.left_widget,
orientation=QtCore.Qt.Vertical)
self.zslider.setInvertedAppearance(True)
self.zslider.setSingleStep(1)
self.zslider.valueChanged.connect(self.update_zlevel)
label_zslider = QtWidgets.QLabel(self.left_widget)
label_zslider.setText("z-level")
self.spinbox_zlevel = QtWidgets.QSpinBox(self.left_widget)
self.spinbox_zlevel.setSingleStep(1)
self.spinbox_zlevel.valueChanged.connect(self.zslider.setValue)
self.zslider.valueChanged.connect(self.spinbox_zlevel.setValue)
hlayout_preprocess.addWidget(label_zslider)
hlayout_preprocess.addWidget(self.zslider)
hlayout_preprocess.addWidget(self.spinbox_zlevel)
self.left_layout.addLayout(hlayout_preprocess)
# preprocess image item
self.glw_preprocess = GraphicsLayoutWidget(self.left_widget)
self.imgitem_preprocess = ImageItem()
self.viewbox_preprocess = self.glw_preprocess.addViewBox()
self.viewbox_preprocess.setAspectLocked(True)
self.viewbox_preprocess.addItem(self.imgitem_preprocess)
self.left_layout.addWidget(self.glw_preprocess)
self.splitter.addWidget(self.left_widget)
# segmentation stuff
self.nuset_model = Nuset()
self.right_layout = QtWidgets.QVBoxLayout(self)
self.right_widget = QtWidgets.QWidget(self.splitter)
self.right_widget.setLayout(self.right_layout)
hlayout_nuset = QtWidgets.QHBoxLayout(self.right_widget)
arg_opts_nuset = \
{
'image': {'ignore': True},
'min_score': {
'minmax': (0.0, 1.0),
'step': 0.05
},
'nms_threshold': {
'minmax': (0.0, 1.0),
'step': 0.05
},
'rescale_ratio': {
'minmax': (0.1, 10.0),
'step': 0.25,
'val': 1.25 # not working if set to 1.0 with pyqtgraph ImageItem for some reason
}
}
self.nuset_controls = \
Function(
self.nuset_model.predict,
arg_opts=arg_opts_nuset,
parent=self.right_widget
)
# self.nuset_controls.button_set.hide()
self.nuset_controls.sig_set_clicked.connect(self.update_segmentation)
self.nuset_controls.set_title("NuSeT Parameters")
hlayout_nuset.addWidget(self.nuset_controls.widget)
arg_opts_postprocess = \
{
'img': {'ignore': True},
'abs_obj_threshold': {
'minmax': (-1, 100),
'step': 2,
},
'rel_obj_threshold': {
'minmax': (0, 100),
'step': 2
},
'obj_connectivity': {
'minmax': (0, 10),
'step': 1
},
'abs_hol_threshold': {
'minmax': (-1, 100),
'step': 2,
},
'rel_hol_threshold': {
'minmax': (0, 100),
'step': 2
},
'hol_connectivity': {
'minmax': (0, 100),
'step': 1
}
}
self.postprocess_controls = \
Function(
get_postprocess,
arg_opts=arg_opts_postprocess,
parent=self.right_widget
)
self.postprocess_controls.button_set.hide()
self.postprocess_controls.sig_changed.connect(self.update_postprocess)
self.postprocess_controls.set_title("Post-process Parameters")
hlayout_nuset.addWidget(self.postprocess_controls.widget)
self.right_layout.addLayout(hlayout_nuset)
self.checkbox_segment_current_plane = QtWidgets.QCheckBox(
self.nuset_controls.widget)
self.checkbox_segment_current_plane.setText(
"Only segment current plane")
self.checkbox_segment_current_plane.setToolTip(
"Performs segmentation for only the current plane, "
"useful for trying out parameters.")
self.checkbox_segment_current_plane.setChecked(True)
self.nuset_controls.vlayout.addWidget(
self.checkbox_segment_current_plane)
self.glw_segmented = GraphicsLayoutWidget(self.right_widget)
self.imgitem_segmented = ImageItem()
self.imgitem_segmented_underlay = ImageItem()
self.viewbox_segmented = self.glw_segmented.addViewBox()
self.viewbox_segmented.setAspectLocked(True)
self.viewbox_segmented.addItem(self.imgitem_segmented)
self.viewbox_segmented.addItem(self.imgitem_segmented_underlay)
# colormaps for the mask overlay plot
cm_cyan = cm.get_cmap(cmap_cyan)
cm_cyan._init()
lut_cyan = (cm_cyan._lut * 255).view(np.ndarray)[128:-5]
self.imgitem_segmented_underlay.setLookupTable(lut_cyan)
# colormaps for the mask overlay plot
cm_magenta = cm.get_cmap(cmap_magenta)
cm_magenta._init()
lut_magenta = (cm_magenta._lut * 255).view(
np.ndarray)[:-5] # so it displays as a mask
self.imgitem_segmented.setLookupTable(lut_magenta)
# allow transparency
# self.imgitem_segmented.setCompositionMode(QtGui.QPainter.CompositionMode_Overlay)
self.imgitem_segmented_underlay.setCompositionMode(
QtGui.QPainter.CompositionMode_SourceOver)
self.imgitem_segmented.setZValue(2)
self.imgitem_segmented.setOpacity(0.5)
self.imgitem_segmented_underlay.setZValue(1)
self.imgitem_segmented_underlay.setOpacity(0.3)
self.slider_underlay_opacity = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.slider_underlay_opacity.setMinimum(0)
self.slider_underlay_opacity.setMaximum(100)
self.slider_underlay_opacity.setValue(30)
self.slider_underlay_opacity.valueChanged.connect(
lambda v: self.imgitem_segmented_underlay.setOpacity(v / 100))
label_underlay_opacity = QtWidgets.QLabel(self.nuset_controls.widget)
label_underlay_opacity.setText("Underlay opacity")
self.nuset_controls.vlayout.addWidget(label_underlay_opacity)
self.nuset_controls.vlayout.addWidget(self.slider_underlay_opacity)
self.slider_mask_opacity = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.slider_mask_opacity.setMinimum(0)
self.slider_mask_opacity.setMaximum(100)
self.slider_mask_opacity.setValue(50)
self.slider_mask_opacity.valueChanged.connect(
lambda v: self.imgitem_segmented.setOpacity(v / 100))
label_segmented_opacity = QtWidgets.QLabel(self.nuset_controls.widget)
label_segmented_opacity.setText("Segmentation opacity")
self.nuset_controls.vlayout.addWidget(label_segmented_opacity)
self.nuset_controls.vlayout.addWidget(self.slider_mask_opacity)
self.combo_blend_mode = QtWidgets.QComboBox(self.nuset_controls.widget)
self.combo_blend_mode.addItems(
['SourceOver', 'Overlay', 'Plus', 'Multiply'])
self.combo_blend_mode.setCurrentIndex(0)
self.combo_blend_mode.currentTextChanged.connect(
lambda opt: self.imgitem_segmented.setCompositionMode(
getattr(QtGui.QPainter, f'CompositionMode_{opt}')))
label_blend_mode = QtWidgets.QLabel(self.nuset_controls.widget)
label_blend_mode.setText('Blend mode:')
self.nuset_controls.vlayout.addWidget(label_blend_mode)
self.nuset_controls.vlayout.addWidget(self.combo_blend_mode)
self.right_layout.addWidget(self.glw_segmented)
self.splitter.addWidget(self.right_widget)
self.export_widget = ExportWidget(self)
self.imgs_projected: List[np.ndarray] = []
self.imgs_preprocessed: List[np.ndarray] = []
self.imgs_segmented: List[np.ndarray] = []
self.imgs_postprocessed: List[np.ndarray] = []
self.input_img: np.ndarray = np.empty(0)
self.zlevel = 0
self.z_max: int = 0
self.process_pool = Pool(cpu_count())
self.error_label = QtWidgets.QLabel(self)
self.error_label.setMaximumHeight(20)
self.error_label.setStyleSheet("font-weight: bold; color: red")
self.vlayout.addWidget(self.error_label)
self.projection_option = ''
self.params_final = None
if viewer_ref is None:
logger.info("Assuming testing mode")
else:
self.vi = ViewerUtils(viewer_ref)
self.vi.viewer.sig_workEnv_changed.connect(self.set_input)
self.set_input(self.vi.viewer.workEnv)
@use_open_file_dialog('Open image file', None, ['*.tiff', '*.tif'])
@present_exceptions('Error', 'Error loading custom input image')
def set_custom_input(self, path, *args):
self.clear_widget()
img = tifffile.imread(path)
self._set_input_image(img.T)
def set_input(self, workEnv: ViewerWorkEnv):
self.clear_widget()
try:
img = workEnv.imgdata._seq
except:
return
self._set_input_image(img)
def _set_input_image(self, img: np.ndarray):
self.input_img = img
if self.input_img.ndim == 4:
self.z_max = self.input_img.shape[3] - 1
else:
self.z_max = 0
self.zslider.valueChanged.disconnect(self.update_zlevel)
self.zslider.setValue(0)
self.zslider.setMaximum(self.z_max)
self.spinbox_zlevel.setMaximum(self.z_max)
self.zslider.valueChanged.connect(self.update_zlevel)
def update_zlevel(self, z: int):
self.zlevel = z
self.sig_zlevel_changed.emit(z)
for imgitem, imglist in zip([
self.imgitem_raw, self.imgitem_preprocess,
self.imgitem_segmented_underlay, self.imgitem_segmented
], [
self.imgs_projected, self.imgs_preprocessed,
self.imgs_preprocessed, self.imgs_postprocessed
]):
if imglist: # set if the list is not empty
if imglist[z].size > 0:
imgitem.setImage(imglist[z])
def update_projection(self):
if not self.input_img.size > 0:
self.error_label.setText("No input image")
return
if self.radio_std.isChecked():
opt = 'std'
elif self.radio_max.isChecked():
opt = 'max'
elif self.radio_mean.isChecked():
opt = 'mean'
if self.projection_option == opt:
return
self.projection_option = opt
func = getattr(np, f'nan{opt}')
logger.info("Updating Projection(s)")
if self.input_img.ndim == 4:
self.imgs_projected = [
func(self.input_img[:, :, :, z], axis=2)
for z in tqdm(range(self.z_max + 1))
]
else:
self.imgs_projected = [func(self.input_img, axis=2)]
self.imgitem_raw.setImage(self.imgs_projected[self.zlevel])
self.error_label.clear()
def update_preprocess(self, params):
if not self.imgs_projected:
self.error_label.setText("Projection Image is Empty")
return
logger.info("Preprocessing Image(s)")
# self.image_preprocesses = [
# get_preprocess(p, **params) for p in tqdm(self.image_projections)
# ]
kwargs = [{'img': img, **params} for img in self.imgs_projected]
self.imgs_preprocessed = self.process_pool.map(wrap_preprocess, kwargs)
self.imgitem_preprocess.setImage(self.imgs_preprocessed[self.zlevel])
self.imgitem_segmented_underlay.setImage(
self.imgs_preprocessed[self.zlevel])
self.error_label.clear()
def update_segmentation(self, params):
if not self.imgs_preprocessed:
self.error_label.setText("Preprocess Image is Empty")
return
logger.info("Segmenting Image(s)")
if not self.checkbox_segment_current_plane.isChecked():
self.imgs_segmented = [
self.nuset_model.predict(img, **params)
for img in tqdm(self.imgs_preprocessed)
]
else:
self.imgs_segmented = [np.empty(0) for i in range(self.z_max + 1)]
self.imgs_segmented[self.zlevel] = self.nuset_model.predict(
self.imgs_preprocessed[self.zlevel], **params)
# postprocess funciton will just return the segmented img if do_postprocess is False
self.update_postprocess(self.postprocess_controls.get_data())
self.params_final = \
{
'method': 'NuSeT',
'projection_option': self.projection_option,
**self.preprocess_controls.get_data(),
**self.nuset_controls.get_data(),
**self.postprocess_controls.get_data(),
}
self.error_label.clear()
def update_postprocess(self, params):
if not self.imgs_segmented:
self.error_label.setText("Segmented Image is Empty")
return
logger.info("Postprocessing Image(s)")
self.imgs_postprocessed = [
get_postprocess(img, **params) for img in tqdm(self.imgs_segmented)
]
self.imgitem_segmented.setImage(self.imgs_postprocessed[self.zlevel])
self.error_label.clear()
def clear_widget(self):
self.imgs_projected.clear()
self.imgs_preprocessed.clear()
self.imgs_segmented.clear()
self.imgs_postprocessed.clear()
self.imgitem_raw.clear()
self.imgitem_preprocess.clear()
self.imgitem_segmented.clear()
self.imgitem_segmented_underlay.clear()
self.radio_std.setChecked(False)
self.radio_max.setChecked(False)
self.radio_mean.setChecked(False)
self.projection_option = ''
def __init__(self, parent, viewer_ref):
QtWidgets.QWidget.__init__(self, parent)
self.vlayout = QtWidgets.QVBoxLayout(self)
self.splitter = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
self.vlayout.addWidget(self.splitter)
self.left_layout = QtWidgets.QVBoxLayout(self)
self.left_widget = QtWidgets.QWidget(self.splitter)
self.left_widget.setLayout(self.left_layout)
hlayout_custom_img = QtWidgets.QHBoxLayout(self.left_widget)
self.lineedit_custom_img_path = QtWidgets.QLineEdit(self.left_widget)
self.lineedit_custom_img_path.setPlaceholderText(
"Path to custom image or stack")
self.lineedit_custom_img_path.setToolTip(
"Use a different image or stack for segmentation, such as an image or stack of nuclei."
)
self.button_use_custom = QtWidgets.QPushButton(self.left_widget)
self.button_use_custom.setMaximumWidth(50)
self.button_use_custom.setText("Set")
hlayout_custom_img.addWidget(self.lineedit_custom_img_path)
hlayout_custom_img.addWidget(self.button_use_custom)
self.left_layout.addLayout(hlayout_custom_img)
hlayout_projection_radios = QtWidgets.QHBoxLayout(self.left_widget)
self.radio_std = QtWidgets.QRadioButton(self.left_widget)
self.radio_std.setText("Std. Deviation")
self.radio_max = QtWidgets.QRadioButton(self.left_widget)
self.radio_max.setText("Max")
self.radio_mean = QtWidgets.QRadioButton(self.left_widget)
self.radio_mean.setText("Mean")
self.projection_option: str = ''
for w in [self.radio_std, self.radio_max, self.radio_mean]:
hlayout_projection_radios.addWidget(w)
w.clicked.connect(self.update_projection)
label_projections = QtWidgets.QLabel(self.left_widget)
label_projections.setText("Choose Input Projection")
label_projections.setStyleSheet("font-weight: bold")
self.left_layout.addWidget(label_projections)
self.left_layout.addLayout(hlayout_projection_radios)
# projection image
self.glw_raw = GraphicsLayoutWidget(self.left_widget)
self.imgitem_raw = ImageItem()
self.viewbox_raw = self.glw_raw.addViewBox()
self.viewbox_raw.setAspectLocked(True)
self.viewbox_raw.addItem(self.imgitem_raw)
self.left_layout.addWidget(self.glw_raw)
hlayout_preprocess = QtWidgets.QHBoxLayout(self.left_widget)
arg_opts_preprocess = \
{
'img': {'ignore': True},
'sigmoid_cutoff': {
'step': 10,
'minmax': (0, 9999.9)
},
'sigmoid_gain': {
'step': 0.01
},
'equalize_lower': {
'step': 0.01,
'minmax': (-1.0, 1.0)
},
'equalize_upper': {
'step': 0.01,
'minmax': (-1.0, 1.0)
}
}
self.preprocess_controls = \
Function(
get_preprocess,
arg_opts=arg_opts_preprocess,
parent=self.left_widget
)
self.preprocess_controls.button_set.hide()
self.preprocess_controls.sig_changed.connect(self.update_preprocess)
self.preprocess_controls.set_title("Pre-process Settings")
hlayout_preprocess.addWidget(self.preprocess_controls.widget)
self.zslider = QtWidgets.QSlider(parent=self.left_widget,
orientation=QtCore.Qt.Vertical)
self.zslider.setInvertedAppearance(True)
self.zslider.setSingleStep(1)
self.zslider.valueChanged.connect(self.update_zlevel)
label_zslider = QtWidgets.QLabel(self.left_widget)
label_zslider.setText("z-level")
self.spinbox_zlevel = QtWidgets.QSpinBox(self.left_widget)
self.spinbox_zlevel.setSingleStep(1)
self.spinbox_zlevel.valueChanged.connect(self.zslider.setValue)
self.zslider.valueChanged.connect(self.spinbox_zlevel.setValue)
hlayout_preprocess.addWidget(label_zslider)
hlayout_preprocess.addWidget(self.zslider)
hlayout_preprocess.addWidget(self.spinbox_zlevel)
self.left_layout.addLayout(hlayout_preprocess)
# preprocess image item
self.glw_preprocess = GraphicsLayoutWidget(self.left_widget)
self.imgitem_preprocess = ImageItem()
self.viewbox_preprocess = self.glw_preprocess.addViewBox()
self.viewbox_preprocess.setAspectLocked(True)
self.viewbox_preprocess.addItem(self.imgitem_preprocess)
self.left_layout.addWidget(self.glw_preprocess)
self.splitter.addWidget(self.left_widget)
# segmentation stuff
self.nuset_model = Nuset()
self.right_layout = QtWidgets.QVBoxLayout(self)
self.right_widget = QtWidgets.QWidget(self.splitter)
self.right_widget.setLayout(self.right_layout)
hlayout_nuset = QtWidgets.QHBoxLayout(self.right_widget)
arg_opts_nuset = \
{
'image': {'ignore': True},
'min_score': {
'minmax': (0.0, 1.0),
'step': 0.05
},
'nms_threshold': {
'minmax': (0.0, 1.0),
'step': 0.05
},
'rescale_ratio': {
'minmax': (0.1, 10.0),
'step': 0.25,
'val': 1.25 # not working if set to 1.0 with pyqtgraph ImageItem for some reason
}
}
self.nuset_controls = \
Function(
self.nuset_model.predict,
arg_opts=arg_opts_nuset,
parent=self.right_widget
)
# self.nuset_controls.button_set.hide()
self.nuset_controls.sig_set_clicked.connect(self.update_segmentation)
self.nuset_controls.set_title("NuSeT Parameters")
hlayout_nuset.addWidget(self.nuset_controls.widget)
arg_opts_postprocess = \
{
'img': {'ignore': True},
'abs_obj_threshold': {
'minmax': (-1, 100),
'step': 2,
},
'rel_obj_threshold': {
'minmax': (0, 100),
'step': 2
},
'obj_connectivity': {
'minmax': (0, 10),
'step': 1
},
'abs_hol_threshold': {
'minmax': (-1, 100),
'step': 2,
},
'rel_hol_threshold': {
'minmax': (0, 100),
'step': 2
},
'hol_connectivity': {
'minmax': (0, 100),
'step': 1
}
}
self.postprocess_controls = \
Function(
get_postprocess,
arg_opts=arg_opts_postprocess,
parent=self.right_widget
)
self.postprocess_controls.button_set.hide()
self.postprocess_controls.sig_changed.connect(self.update_postprocess)
self.postprocess_controls.set_title("Post-process Parameters")
hlayout_nuset.addWidget(self.postprocess_controls.widget)
self.right_layout.addLayout(hlayout_nuset)
self.checkbox_segment_current_plane = QtWidgets.QCheckBox(
self.nuset_controls.widget)
self.checkbox_segment_current_plane.setText(
"Only segment current plane")
self.checkbox_segment_current_plane.setToolTip(
"Performs segmentation for only the current plane, "
"useful for trying out parameters.")
self.checkbox_segment_current_plane.setChecked(True)
self.nuset_controls.vlayout.addWidget(
self.checkbox_segment_current_plane)
self.glw_segmented = GraphicsLayoutWidget(self.right_widget)
self.imgitem_segmented = ImageItem()
self.imgitem_segmented_underlay = ImageItem()
self.viewbox_segmented = self.glw_segmented.addViewBox()
self.viewbox_segmented.setAspectLocked(True)
self.viewbox_segmented.addItem(self.imgitem_segmented)
self.viewbox_segmented.addItem(self.imgitem_segmented_underlay)
# colormaps for the mask overlay plot
cm_cyan = cm.get_cmap(cmap_cyan)
cm_cyan._init()
lut_cyan = (cm_cyan._lut * 255).view(np.ndarray)[128:-5]
self.imgitem_segmented_underlay.setLookupTable(lut_cyan)
# colormaps for the mask overlay plot
cm_magenta = cm.get_cmap(cmap_magenta)
cm_magenta._init()
lut_magenta = (cm_magenta._lut * 255).view(
np.ndarray)[:-5] # so it displays as a mask
self.imgitem_segmented.setLookupTable(lut_magenta)
# allow transparency
# self.imgitem_segmented.setCompositionMode(QtGui.QPainter.CompositionMode_Overlay)
self.imgitem_segmented_underlay.setCompositionMode(
QtGui.QPainter.CompositionMode_SourceOver)
self.imgitem_segmented.setZValue(2)
self.imgitem_segmented.setOpacity(0.5)
self.imgitem_segmented_underlay.setZValue(1)
self.imgitem_segmented_underlay.setOpacity(0.3)
self.slider_underlay_opacity = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.slider_underlay_opacity.setMinimum(0)
self.slider_underlay_opacity.setMaximum(100)
self.slider_underlay_opacity.setValue(30)
self.slider_underlay_opacity.valueChanged.connect(
lambda v: self.imgitem_segmented_underlay.setOpacity(v / 100))
label_underlay_opacity = QtWidgets.QLabel(self.nuset_controls.widget)
label_underlay_opacity.setText("Underlay opacity")
self.nuset_controls.vlayout.addWidget(label_underlay_opacity)
self.nuset_controls.vlayout.addWidget(self.slider_underlay_opacity)
self.slider_mask_opacity = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.slider_mask_opacity.setMinimum(0)
self.slider_mask_opacity.setMaximum(100)
self.slider_mask_opacity.setValue(50)
self.slider_mask_opacity.valueChanged.connect(
lambda v: self.imgitem_segmented.setOpacity(v / 100))
label_segmented_opacity = QtWidgets.QLabel(self.nuset_controls.widget)
label_segmented_opacity.setText("Segmentation opacity")
self.nuset_controls.vlayout.addWidget(label_segmented_opacity)
self.nuset_controls.vlayout.addWidget(self.slider_mask_opacity)
self.combo_blend_mode = QtWidgets.QComboBox(self.nuset_controls.widget)
self.combo_blend_mode.addItems(
['SourceOver', 'Overlay', 'Plus', 'Multiply'])
self.combo_blend_mode.setCurrentIndex(0)
self.combo_blend_mode.currentTextChanged.connect(
lambda opt: self.imgitem_segmented.setCompositionMode(
getattr(QtGui.QPainter, f'CompositionMode_{opt}')))
label_blend_mode = QtWidgets.QLabel(self.nuset_controls.widget)
label_blend_mode.setText('Blend mode:')
self.nuset_controls.vlayout.addWidget(label_blend_mode)
self.nuset_controls.vlayout.addWidget(self.combo_blend_mode)
self.right_layout.addWidget(self.glw_segmented)
self.splitter.addWidget(self.right_widget)
self.export_widget = ExportWidget(self)
self.imgs_projected: List[np.ndarray] = []
self.imgs_preprocessed: List[np.ndarray] = []
self.imgs_segmented: List[np.ndarray] = []
self.imgs_postprocessed: List[np.ndarray] = []
self.input_img: np.ndarray = np.empty(0)
self.zlevel = 0
self.z_max: int = 0
self.process_pool = Pool(cpu_count())
self.error_label = QtWidgets.QLabel(self)
self.error_label.setMaximumHeight(20)
self.error_label.setStyleSheet("font-weight: bold; color: red")
self.vlayout.addWidget(self.error_label)
self.projection_option = ''
self.params_final = None
if viewer_ref is None:
logger.info("Assuming testing mode")
else:
self.vi = ViewerUtils(viewer_ref)
self.vi.viewer.sig_workEnv_changed.connect(self.set_input)
self.set_input(self.vi.viewer.workEnv)
from pyqtgraph.console import ConsoleWidget
def f(a: int = 1, b: float = 3.14, c: str = 'yay', d: bool = True):
pass
if __name__ == '__main__':
app = QtWidgets.QApplication([])
opts = \
{
'b':
{
'use_slider': True,
'minmax': (0, 100),
'step': 1,
'suffix': '%',
'typ': int,
'tooltip': 'yay tooltips'
}
}
func = Function(f, arg_opts=opts)
func.widget.show()
console = ConsoleWidget(parent=func.widget, namespace={'this': func})
func.vlayout.addWidget(console)
app.exec()