def multiprocessing_settings_block(main_widget):
data_handler = main_widget.data_handler
return SettingBlockModule("Multiprocessing Settings", [
IntInput(
display_name="Number of spatial boxes:",
program_name="total_num_spatial_boxes",
on_change_function=lambda x, y: data_handler.change_box_param(
x, y),
default_val=
data_handler.box_params[
"total_num_spatial_boxes"],
tool_tip="Used to break the calculation into smaller overlapping parts.\n "
"This number must be square. The number of spatial boxes per side will be equal to square of this number.",
min=1, max=10000, step=1)
,
IntInput(
display_name="Spatial overlap:",
program_name="spatial_overlap",
on_change_function=lambda x, y: data_handler.change_box_param(x, y),
default_val=
data_handler.box_params[
"spatial_overlap"],
tool_tip="Number of pixels to overlap each box.",
min=1, max=10000, step=1)])
def dataset_setting_block(main_widget):
data_handler = main_widget.data_handler
return SettingBlockModule("Advanced Settings",
[BoolInput(display_name="Slice stack:",
program_name="slice_stack",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=data_handler.dataset_params[
"slice_stack"],
tool_tip="Used to Select only "
"every x timestep",
display_tool_tip=False),
IntInput(display_name="Slice every:",
program_name="slice_every",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=data_handler.dataset_params[
"slice_every"],
tool_tip="Select every x timesteps",
min=1, max=100, step=1),
IntInput(display_name="Slice start:",
program_name="slice_start",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
tool_tip="Start selecting on x timestep",
default_val=data_handler.dataset_params[
"slice_start"],
min=0, max=10000, step=1)
])
def dataset_setting_block_crop(main_widget):
data_handler = main_widget.data_handler
return SettingBlockModule("Crop Settings",
[BoolInput(display_name="Crop stack:",
program_name="crop_stack",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=data_handler.dataset_params[
"crop_stack"],
tool_tip="Used to crop image stack",
display_tool_tip=False),
IntRangeInput(display_name="Crop X:",
program_name="crop_y",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=data_handler.dataset_params[
"crop_y"],
tool_tip="Crop rows",
min=0, max=10000, step=1),
IntRangeInput(display_name="Crop Y:",
# different because the way we display images is weird x is first dim y is second dim
program_name="crop_x",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=data_handler.dataset_params[
"crop_x"],
tool_tip="Crop columns",
min=0, max=100000, step=1),
] + ([BoolInput(
display_name="Split into Time Blocks(recomended):",
program_name="trial_split",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=data_handler.dataset_params[
"trial_split"],
tool_tip="Splits the timesteps into separate time blocks better for processing "
"every x timestep. This setting is recomended for all large datasets",
display_tool_tip=False),
IntInput(
display_name="Time Block Length",
program_name="trial_length",
on_change_function=lambda x,
y: data_handler.change_dataset_param(
x, y),
default_val=
data_handler.dataset_params[
"trial_length"],
tool_tip="Length of each timeblock",
display_tool_tip=False,
min=25,
max=2000,
step=1)] if
data_handler.dataset_params[
"original_folder_trial_split"] != "" else []))
def filter_setting_block(main_widget):
data_handler = main_widget.data_handler
return SettingBlockModule("Filter Settings",
[BoolInput(display_name="Local Spatial Denoising:",
program_name="localSpatialDenoising",
on_change_function=lambda x,
y: data_handler.change_filter_param(
x, y),
default_val=data_handler.filter_params[
"localSpatialDenoising"],
tool_tip="Local Spatial Denoising helps smooth out the noise in the data by averaging ",
),
BoolInput(
display_name="Z-score:",
program_name="z_score",
on_change_function=lambda x,
y: data_handler.change_filter_param(
x, y),
default_val=
data_handler.filter_params["z_score"],
tool_tip="Applies a z-score for each pixel across each of the timesteps",
),
BoolInput(display_name="Histogram Equalization Method:",
program_name="hist_eq",
on_change_function=lambda x,
y: data_handler.change_filter_param(
x, y),
default_val=data_handler.filter_params[
"hist_eq"],
tool_tip="Applies a histogram equalization method(a more advanced z score",
),
BoolInput(display_name="Median filter:",
program_name="median_filter",
on_change_function=lambda x,
y: data_handler.change_filter_param(
x, y),
default_val=data_handler.filter_params[
"median_filter"],
tool_tip="Applies a 3D median filter to each timestep. This helps denoise the image. ",
),
IntInput(
display_name="Median filter size:",
program_name="median_filter_size",
on_change_function=lambda x,
y: data_handler.change_filter_param(
x, y),
default_val=
data_handler.filter_params[
"median_filter_size"],
tool_tip="The size of the 3D median filter. Recomended size: 3",
min=1, max=50, step=1),
BoolInput(display_name="PCA:",
program_name="pca",
on_change_function=lambda x,
y: data_handler.change_filter_param(
x, y),
default_val=data_handler.filter_params[
"pca"],
tool_tip="Applies PCA decomposition to the dataset (PCA runs after other filters). \n Both speeds along other calculations and helps remove background noise. \n Time traces are still calculated on filtered stack not PCA stack.",
),
# FloatInput(
# display_name="PCA expression threshold",
# program_name="pca_threshold",
# on_change_function=lambda x,
# y: data_handler.change_filter_param(
# x, y),
# default_val=
# data_handler.filter_params[
# "pca_threshold"],
# tool_tip="The percentage of the variance that the PCA will express",
# min=0.001, max=.999, step=.001),
])
def roi_advanced_settings_block(main_widget):
# TODO fix input into spatial box number
data_handler = main_widget.data_handler
return SettingBlockModule("Advanced Settings",
[IntInput(display_name="Number of eigen vectors:",
program_name="num_eig",
on_change_function=lambda x,
y: data_handler.change_eigen_param(
x, y),
default_val=data_handler.eigen_params[
"num_eig"],
tool_tip="Number of eigen vectors to generate. Increase if eigen norm image isn't showing all rois",
min=1, max=10000, step=1),
FloatInput(display_name="Eigen threshold value:",
program_name="eigen_threshold_value",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=
data_handler.roi_extraction_params[
"eigen_threshold_value"],
tool_tip="Number of eigen vectors to select for each ROI. Multiply number of trials by the number of eigen vectors \n if this number is below 300, then it might help to increase this value to .3 or .5",
min=0, max=1, step=.01),
# FloatInput(display_name="Elbow threshold value:",
# program_name="elbow_threshold_value",
# on_change_function=lambda x,
# y: data_handler.change_roi_extraction_param(
# x, y),
# default_val=
# data_handler.roi_extraction_params[
# "elbow_threshold_value"],
# tool_tip="Number of eigen vectors to select at each point",
# min=0, max=1.5, step=.01),
# BoolInput(
# display_name="Merge ROIs:",
# program_name="merge",
# on_change_function=lambda x,
# y: data_handler.change_roi_extraction_param(
# x, y),
# default_val=
# data_handler.roi_extraction_params[
# "merge"],
# tool_tip="Whether to merge rois with similar time traces"),
IntInput(display_name="ROI Eccentricity Threshold:",
program_name="roi_circ_threshold",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=
data_handler.roi_extraction_params[
"roi_circ_threshold"],
tool_tip="Thresholds the rois based on how circular they are. Lowering the number would allow more ROIs through",
min=0, max=100, step=1),
# IntInput(display_name="Number of connections:",
# program_name="connections",
# on_change_function=lambda x,
# y: data_handler.change_eigen_param(
# x, y),
# default_val=data_handler.eigen_params[
# "connections"],
# tool_tip="Number of eigen vectors to generate",
# min=1, max=10000, step=1),
# IntInput(display_name="accuracy:",
# program_name="accuracy",
# on_change_function=lambda x,
# y: data_handler.change_eigen_param(
# x, y),
# default_val=data_handler.eigen_params[
# "accuracy"],
# tool_tip="Number of eigen vectors to generate",
# min=1, max=10000, step=1),
# IntInput(display_name="Number of knn:",
# program_name="knn",
# on_change_function=lambda x,
# y: data_handler.change_eigen_param(
# x, y),
# default_val=data_handler.eigen_params[
# "knn"],
# tool_tip="Number of eigen vectors to generate",
# min=1, max=10000, step=1),
IntInput(display_name="Eigen Accuracy:",
program_name="eigen_accuracy",
on_change_function=lambda x,
y: data_handler.change_eigen_param(
x, y),
default_val=data_handler.eigen_params[
"eigen_accuracy"],
tool_tip="10^-x accuracy for each eigen vector, If there are lines in the eigen norm image increase this to 7 or 8",
min=1, max=10000, step=1),
IntInput(display_name="Number of iterations:",
program_name="max_iter",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=data_handler.roi_extraction_params[
"max_iter"],
tool_tip="The number of iterations of the algorithm to preform. Increase if not detecting all rois but they are present in the eigen norm image",
min=1, max=10000, step=1),
# IntInput(display_name="Number of time steps:",
# program_name="total_num_time_steps",
# on_change_function=lambda x,
# y: data_handler.change_box_param(
# x, y),
# default_val=data_handler.box_params[
# "total_num_time_steps"],
# tool_tip=
# "Number of time steps to break" +
# "the processing into",
# min=1, max=10000, step=1),
#
]
)
def roi_extraction_settings_block(main_widget):
# TODO fix input into spatial box number
data_handler = main_widget.data_handler
return SettingBlockModule("ROI Extraction Settings",
[
IntInput(
display_name="Max Number of ROIs per spatial box:",
program_name="num_rois",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=data_handler.roi_extraction_params[
"num_rois"],
tool_tip="Max number of ROIs to select for each spatial box, increase this number if not detecting all ROIs",
min=0, max=10000, step=1),
IntInput(
display_name="ROI size minimum:",
program_name="roi_size_min",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=
data_handler.roi_extraction_params[
"roi_size_min"],
tool_tip="Minimum size in pixels for a region of interest",
min=1, max=10000, step=1),
IntInput(
display_name="ROI size maximum:",
program_name="roi_size_max",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=
data_handler.roi_extraction_params[
"roi_size_max"],
tool_tip="Maximum size in pixels for a region of interest",
min=1, max=1000000, step=1),
# BoolInput(
# display_name="Run refinement step:",
# program_name="refinement",
# on_change_function=lambda x,
# y: data_handler.change_roi_extraction_param(
# x, y),
# default_val=
# data_handler.roi_extraction_params[
# "refinement"],
# tool_tip="Whether to run the refinement step, greatly improves results"),
FloatInput(
display_name="Merge temporal coefficient:",
program_name="merge_temporal_coef",
on_change_function=lambda x,
y: data_handler.change_roi_extraction_param(
x, y),
default_val=
data_handler.roi_extraction_params[
"merge_temporal_coef"],
tool_tip="The coefficient that determines if two overlapping regions are merged based on their temporal correlation",
min=0, max=1, step=.01)
# BoolInput(
# display_name="Fill holes:",
# program_name="fill_holes",
# on_change_function=lambda x,
# y: data_handler.change_roi_extraction_param(
# x, y),
# default_val=
# data_handler.roi_extraction_params[
# "fill_holes"],
# tool_tip="Whether to fill holes in each roi"),
#
]
)
def __init__(self, main_widget):
self.main_widget = main_widget
self.image_view = ROIPaintImageViewModule(main_widget, self, False)
self.image_view.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.roi_unconnected = QErrorMessage(self.main_widget.main_window)
# This part creates the top left settings/roi list view in two tabs
self.tab_selector_roi = QTabWidget()
# self.tab_selector_roi.setStyleSheet("QTabWidget {font-size: 20px;}")
# ROI modification Tab
roi_modification_tab = QWidget()
roi_modification_tab.setStyleSheet("margin:0px; padding: 0px;")
roi_modification_tab_layout = QVBoxLayout()
roi_modification_tab_layout.setContentsMargins(1, 1, 1, 1)
roi_modification_tab_layout_top = QVBoxLayout()
roi_modification_tab_layout_top.setContentsMargins(0, 0, 0, 0)
roi_modification_tab_layout.addLayout(roi_modification_tab_layout_top)
display_settings = self.image_view.createSettings()
display_settings.setStyleSheet("QWidget {border: 2px solid #32414B;}")
roi_modification_tab_layout.addWidget(display_settings)
roi_modification_tab.setLayout(roi_modification_tab_layout)
self.roi_list_module = ROIListModule(main_widget.data_handler,
self,
select_multiple=False,
display_time=False)
roi_modification_tab_layout.addWidget(self.roi_list_module)
roi_modification_button_top_layout = QHBoxLayout()
roi_modification_button_top_layout.setContentsMargins(2, 2, 2, 2)
roi_modification_button_top_widget = QWidget()
roi_modification_button_top_widget.setStyleSheet(
"QWidget {border: 0px solid #32414B;}")
roi_modification_button_top_widget.setLayout(
roi_modification_button_top_layout)
# roi_modification_tab_layout.addLayout(roi_modification_button_top_layout)
add_new_roi = QPushButton(text="Create ROI from\nMask (D)")
add_new_roi.clicked.connect(lambda x: self.add_new_roi())
add_new_roi.setToolTip(
"Use this button to create a new ROI from mask. \n"
"ROI is added to bottiom of ROI list")
add_to_roi = QPushButton(text="Add Mask to \nSelected ROI (A)")
add_to_roi.clicked.connect(lambda x: self.modify_roi(
self.roi_list_module.current_selected_roi, "add"))
add_to_roi.setToolTip("Use this button to add the current mask to"
" the selected ROI. \n"
"Select an roi in the ROI list below")
sub_to_roi = QPushButton(text="Subtract Mask from\nSelected ROI (S)")
sub_to_roi.clicked.connect(lambda x: self.modify_roi(
self.roi_list_module.current_selected_roi, "subtract"))
sub_to_roi.setToolTip(
"Use this button to subtract the current mask from"
" the selected ROI. \n"
"Select an roi in the ROI list below")
delete_roi = QPushButton(text="Delete Selected\nROI (F)")
delete_roi.setToolTip("Use this button to delete the selected ROI. \n"
"Select an roi in the ROI list below")
delete_roi.clicked.connect(lambda x: self.delete_roi(
self.roi_list_module.current_selected_roi))
roi_modification_button_top_layout.addWidget(add_new_roi)
roi_modification_button_top_layout.addWidget(add_to_roi)
roi_modification_button_top_layout.addWidget(sub_to_roi)
roi_modification_button_top_layout.addWidget(delete_roi)
add_to_roi.setStyleSheet("QWidget {border: 0px solid #32414B;}")
sub_to_roi.setStyleSheet("QWidget {border: 0px solid #32414B;}")
add_new_roi.setStyleSheet("QWidget {border: 0px solid #32414B;}")
delete_roi.setStyleSheet("QWidget {border: 0px solid #32414B;}")
# Paint Selection button group
painter_button_group = QButtonGroup()
self.off_button = QRadioButton(text="Off (Q)")
self.off_button.setChecked(True)
self.off_button.setToolTip("Turns off the mask brush")
self.on_button = QRadioButton(text="Add to Mask (W)")
self.on_button.setToolTip(
"Turns on the selector brush, draw on the image by right clicking")
self.sub_button = QRadioButton(text="Subtract from Mask (E)")
self.sub_button.setToolTip(
"Turns the selector brush to subtract mode. Removing currently selected pixels"
)
self.magic_wand = QRadioButton(text="Magic Wand (R)")
self.magic_wand.setToolTip(
"Turns the Mask brush to magic wand mode. Click on where you believe \n"
"there should be an ROI, and it will attempt to create one for you.\n Note just click one at a time. "
)
self.off_button.setStyleSheet("QWidget {border: 0px solid #32414B;}")
self.on_button.setStyleSheet("QWidget {border: 0px solid #32414B;}")
self.sub_button.setStyleSheet("QWidget {border: 0px solid #32414B;}")
self.magic_wand.setStyleSheet("QWidget {border: 0px solid #32414B;}")
painter_button_group.addButton(self.off_button)
painter_button_group.addButton(self.on_button)
painter_button_group.addButton(self.sub_button)
painter_button_group.addButton(self.magic_wand)
self.off_button.clicked.connect(
lambda x: self.image_view.setSelectorBrushType("off"))
self.on_button.clicked.connect(
lambda x: self.image_view.setSelectorBrushType("add"))
self.sub_button.clicked.connect(
lambda x: self.image_view.setSelectorBrushType("subtract"))
self.magic_wand.clicked.connect(
lambda x: self.image_view.setSelectorBrushType("magic"))
painter_widget = QWidget()
painter_layout = QVBoxLayout()
painter_widget.setLayout(painter_layout)
label = QLabel(text="Mask Brush (green): ")
label.setStyleSheet("QWidget {border: 0px solid #32414B;}")
painter_layout_sub_1 = QHBoxLayout()
painter_layout_sub_1.addWidget(label)
painter_layout_sub_1.addWidget(self.off_button)
painter_layout_sub_2 = QHBoxLayout()
painter_layout_sub_2.addWidget(self.on_button)
painter_layout_sub_2.addWidget(self.magic_wand)
painter_layout_sub_3 = QHBoxLayout()
painter_layout_sub_3.addWidget(self.sub_button)
painter_layout.addLayout(painter_layout_sub_1)
painter_layout.addLayout(painter_layout_sub_2)
painter_layout.addLayout(painter_layout_sub_3)
self._brush_size_options = OptionInput(
"Brush Size:", "", lambda x, y: self.image_view.setBrushSize(y), 1,
"Sets the brush size",
["1", "3", "5", "7", "9", "11", "15", "21", "27", "35"])
self._brush_size_options.setStyleSheet(
"QWidget {border: 0px solid #32414B;}")
painter_layout_sub_3.addWidget(self._brush_size_options)
clear_from_selection = QPushButton(text="Clear Mask (T)")
clear_from_selection.setStyleSheet(
"QWidget {border: 0px solid #32414B;}")
clear_from_selection.clicked.connect(
lambda x: self.image_view.clearPixelSelection())
painter_layout.addWidget(clear_from_selection)
roi_modification_button_top_widget.setStyleSheet(
"QWidget {border: 2px solid #32414B; font-size: %dpx}" %
(self.main_widget.scale * 20))
painter_widget.setStyleSheet("QWidget {border: 2px solid #32414B;}")
roi_modification_tab_layout_top.addWidget(painter_widget)
roi_modification_tab_layout_top.addWidget(
roi_modification_button_top_widget)
recalc_time_traces_button = QPushButton(text="Recalculate Time Traces")
recalc_time_traces_button.clicked.connect(
lambda: self.update_time_traces())
roi_modification_tab_layout.addWidget(recalc_time_traces_button)
# ROI Settings Tab
process_button = QPushButton()
process_button.setText("Apply Settings")
self.thread = ROIExtractionThread(main_widget, process_button,
self.roi_list_module, self)
self.main_widget.thread_list.append(self.thread)
self.time_trace_thread = TimeTraceCalculateThread(
main_widget, process_button, self.roi_list_module)
self.main_widget.thread_list.append(self.time_trace_thread)
process_button.clicked.connect(lambda: self.thread.runThread())
self.roi_settings = QWidget()
self.roi_settings_layout = QVBoxLayout()
self.roi_settings_layout.setContentsMargins(2, 2, 2, 2)
self.roi_settings.setLayout(self.roi_settings_layout)
settings = roi_extraction_settings(main_widget)
self.roi_settings_layout.addWidget(settings)
self.roi_settings_layout.addWidget(process_button)
# adding the tabs to the window
self.tab_selector_roi.addTab(self.roi_settings, "ROI Creation")
self.tab_selector_roi.addTab(roi_modification_tab, "ROI Modification")
# self.tab_selector_roi.setMaximumWidth(435)
# self.tab_selector_roi.setMinimumWidth(435)
# Eigen vector viewer if dev mode is enabled
if self.main_widget.dev:
self.eigen_view = QWidget()
self.eigen_view_layout = QVBoxLayout()
self.eigen_view_box_input = IntInput("Box Number", "", None, 0, "",
0, 100, 1, False)
self.eigen_view_number_input = IntInput("Vector Number", "", None,
0, "", 0, 100, 1, False)
self.eigen_view_trial_input = IntInput("Trial Number", "", None, 0,
"", 0, 100, 1, False)
view_eigen_vector_button = QPushButton("View Eigen Vector")
view_eigen_vector_button.clicked.connect(
lambda x: self.view_eigen_vector())
self.eigen_view_layout.addWidget(self.eigen_view_box_input)
self.eigen_view_layout.addWidget(self.eigen_view_number_input)
self.eigen_view_layout.addWidget(self.eigen_view_trial_input)
self.eigen_view_layout.addWidget(view_eigen_vector_button)
self.eigen_view.setLayout(self.eigen_view_layout)
self.tab_selector_roi.addTab(self.eigen_view, "View Eigen Vectors")
# If ROIs are loaded, add them to display
# Tab selector for the time trace window
tab_selector_time_trace = QTabWidget()
# tab_selector_time_trace.setStyleSheet("QTabWidget {font-size: 20px;}")
tab_selector_time_trace.setMaximumHeight(220)
# plot of time traces
self.time_plot = pg.PlotWidget()
self.time_plot.getPlotItem().getViewBox().setMouseEnabled(True, False)
self.time_plot.showGrid(x=True, y=True, alpha=0.3)
tab_selector_time_trace.addTab(self.time_plot, "Time Trace Plot")
# Setting window for time traces
time_trace_settings = QWidget()
time_trace_settings_layout = QVBoxLayout()
time_trace_settings_layout.setContentsMargins(0, 0, 0, 0)
time_trace_settings.setLayout(time_trace_settings_layout)
self.time_trace_type = OptionInput(
"Time Trace Type",
"",
lambda x, y: self.deselectRoiTime(),
default_index=0,
tool_tip="Select way to calculate time trace,"
" \ncheck github for more details",
val_list=list(
self.data_handler.time_trace_possibilities_functions.keys()))
time_trace_settings_layout.addWidget(self.time_trace_type, stretch=1)
# A list widget to select what trials to calculate/display time traces for
self._time_trace_trial_select_list = TrialListWidget(False)
self._time_trace_trial_select_list.setMinimumHeight(115)
self._time_trace_trial_select_list.set_items_from_list(
self.data_handler.trials_all,
self.data_handler.trials_loaded_time_trace_indices)
if not len(self.data_handler.trials_loaded) == 1 and not \
self.data_handler.dataset_params["single_file_mode"] and not \
self.data_handler.dataset_params["trial_split"]:
time_trace_settings_layout.addWidget(
self._time_trace_trial_select_list, stretch=5)
time_trace_update_button = QPushButton("Update Time Traces")
time_trace_settings_layout.addWidget(time_trace_update_button)
time_trace_update_button.clicked.connect(
lambda x: self.update_time_traces())
tab_selector_time_trace.addTab(time_trace_settings,
"Time Trace Settings")
self.updateTab()
super().__init__("ROI Extraction",
column_1=[self.tab_selector_roi],
column_2=[self.image_view, tab_selector_time_trace],
column_2_display=True,
horiz_moveable=True)
self._brush_size_options.setMinimumHeight(
int(30 * ((self.logicalDpiX() / 96.0 - 1) / 2 + 1)))