suite2p.gui package

Submodules

suite2p.gui.buttons module

class suite2p.gui.buttons.QuadButton(bid, Text, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

custom QPushButton class for quadrant plotting requires buttons to put into a QButtonGroup (parent.quadbtns)

allows only 1 button to pressed at a time

press(parent, bid)

class suite2p.gui.buttons.SizeButton(bid, Text, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

buttons to make trace box bigger or smaller

press(parent)

class suite2p.gui.buttons.TopButton(bid, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

selection of top neurons

press(parent)

top_selection(parent)

suite2p.gui.buttons.make_cellnotcell(parent)

buttons for cell / not cell views at top

suite2p.gui.buttons.make_quadrants(parent)

make quadrant buttons

suite2p.gui.buttons.make_selection(parent)

buttons to draw a square on view

suite2p.gui.classgui module

class suite2p.gui.classgui.ListChooser(Text, parent=None)

Bases: PyQt5.QtWidgets.QDialog

apply_class(parent)

build_classifier(parent)

exit_list()

load_cell()

load_text()

save_default(parent)

suite2p.gui.classgui.activate(parent, inactive)

suite2p.gui.classgui.add_to(parent)

suite2p.gui.classgui.class_activated(parent)

suite2p.gui.classgui.class_default(parent)

suite2p.gui.classgui.class_file(parent)

suite2p.gui.classgui.class_masks(parent)

suite2p.gui.classgui.disable(parent)

suite2p.gui.classgui.load(parent, name)

suite2p.gui.classgui.load_classifier(parent)

suite2p.gui.classgui.load_data(parent, keys, trainfiles)

suite2p.gui.classgui.load_default_classifier(parent)

suite2p.gui.classgui.load_list(parent)

suite2p.gui.classgui.load_s2p_classifier(parent)

suite2p.gui.classgui.make_buttons(parent, b0)

suite2p.gui.classgui.reset_default(parent)

suite2p.gui.classgui.save(parent, train_stats, train_iscell, keys)

suite2p.gui.classgui.save_list(parent)

suite2p.gui.classgui.save_model(name, train_stats, train_iscell, keys)

suite2p.gui.drawroi module

class suite2p.gui.drawroi.ROIDraw(parent)

Bases: PyQt5.QtWidgets.QMainWindow

add_ROI(pos=None)

check_proc(event)

closeEvent(self, QCloseEvent)

close_GUI()

create_masks_of_cells(mean_img)

keyPressEvent(self, QKeyEvent)

mouse_moved(pos)

normalize_img_add_masks()

plot_clicked(event)

plot_trace()

proc_ROI()

class suite2p.gui.drawroi.ViewButton(bid, Text, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

press(parent, bid)

suite2p.gui.drawroi.masks_and_traces(ops, stat_manual, stat_orig)

main extraction function inputs: ops and stat creates cell and neuropil masks and extracts traces returns: F (ROIs x time), Fneu (ROIs x time), F_chan2, Fneu_chan2, ops, stat F_chan2 and Fneu_chan2 will be empty if no second channel

class suite2p.gui.drawroi.sROI(iROI, parent=None, pos=None, diameter=None, color=None, yrange=None, xrange=None)

Bases: object

draw(parent, imy, imx, dy, dx)

position(parent)

remove(parent)

suite2p.gui.graphics module

suite2p.gui.graphics.ROI_index(ops, stat)

matrix Ly x Lx where each pixel is an ROI index (-1 if no ROI present)

class suite2p.gui.graphics.TraceBox(parent=None, border=None, lockAspect=False, enableMouse=True, invertY=False, enableMenu=True, name=None, invertX=False)

Bases: pyqtgraph.graphicsItems.PlotItem.PlotItem.PlotItem

mouseDoubleClickEvent(self, QGraphicsSceneMouseEvent)

zoom_plot()

class suite2p.gui.graphics.ViewBox(parent=None, border=None, lockAspect=False, enableMouse=True, invertY=False, enableMenu=True, name=None, invertX=False)

Bases: pyqtgraph.graphicsItems.ViewBox.ViewBox.ViewBox

mouseClickEvent(ev)

mouseDoubleClickEvent(self, QGraphicsSceneMouseEvent)

mouseDragEvent(ev, axis=None)

zoom_plot()

suite2p.gui.graphics.init_range(parent)

suite2p.gui.gui2p module

class suite2p.gui.gui2p.MainWindow(statfile=None)

Bases: PyQt5.QtWidgets.QMainWindow

ROI_position()

ROI_remove()

ROI_selection()

ROIs_on(state)

dragEnterEvent(self, QDragEnterEvent)

dropEvent(self, QDropEvent)

ichosen_stats()

keyPressEvent(self, QKeyEvent)

make_buttons()

make_graphics(b0)

mode_change(i)

changes the activity mode that is used when multiple neurons are selected or in visualization windows like rastermap or for correlation computation!

activityMode = 0 : F 1 : Fneu 2 : F - 0.7 * Fneu (default) 3 : spks

uses binning set by self.bin

number_chosen()

plot_clicked(event)

left-click chooses a cell, right-click flips cell to other view

select_cells(ypix, xpix)

top_number_chosen()

update_plot()

zoom_cell(state)

zoom_to_cell()

suite2p.gui.gui2p.run(statfile=None)

suite2p.gui.io module

suite2p.gui.io.enable_views_and_classifier(parent)

suite2p.gui.io.export_fig(parent)

suite2p.gui.io.load_NWB(parent)

suite2p.gui.io.load_again(parent, Text)

suite2p.gui.io.load_behavior(parent)

suite2p.gui.io.load_custom_mask(parent)

suite2p.gui.io.load_dialog(parent)

suite2p.gui.io.load_dialog_NWB(parent)

suite2p.gui.io.load_dialog_folder(parent)

suite2p.gui.io.load_files(name)

give stat.npy path and load all needed files for suite2p

suite2p.gui.io.load_folder(parent)

suite2p.gui.io.load_proc(parent)

suite2p.gui.io.load_to_GUI(parent, basename, procs)

suite2p.gui.io.make_masks_and_enable_buttons(parent)

suite2p.gui.io.save_iscell(parent)

suite2p.gui.io.save_mat(parent)

suite2p.gui.io.save_merge(parent)

suite2p.gui.io.save_redcell(parent)

suite2p.gui.masks module

class suite2p.gui.masks.ColorButton(bid, Text, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

press(parent, bid)

suite2p.gui.masks.add_roi(parent, n, i)

add roi n to view i

suite2p.gui.masks.beh_masks(parent)

suite2p.gui.masks.chan2_masks(parent)

suite2p.gui.masks.chan2_prob(parent)

suite2p.gui.masks.cmap_change(parent)

suite2p.gui.masks.corr_masks(parent)

suite2p.gui.masks.custom_masks(parent)

suite2p.gui.masks.draw_colorbar(colormap='hsv')

suite2p.gui.masks.draw_masks(parent)

creates RGB masks using stat and puts them in M0 or M1 depending on whether or not iscell is True for a given ROI :param ops: mean_image, Vcorr :param stat: xpix,ypix :param iscell: vector with True if ROI is cell :param ops_plot: plotROI, view, color, randcols

outputs:

M0: ROIs that are True in iscell M1: ROIs that are False in iscell

suite2p.gui.masks.flip_for_class(parent, iscell)

suite2p.gui.masks.flip_plot(parent)

suite2p.gui.masks.flip_roi(parent)

flips roi to other plot there are 3 levels of overlap so this may be buggy if more than 3 cells are on top of each other

suite2p.gui.masks.hsv2rgb(cols)

suite2p.gui.masks.init_masks(parent)

creates RGB masks using stat and puts them in M0 or M1 depending on whether or not iscell is True for a given ROI :param ops: mean_image, Vcorr :param stat: xpix,ypix,xext,yext :param iscell: vector with True if ROI is cell :param ops_plot: plotROI, view, color, randcols

outputs:

M0: ROIs that are True in iscell M1: ROIs that are False in iscell

suite2p.gui.masks.istat_hsv(istat)

suite2p.gui.masks.istat_transform(istat, colormap='hsv')

suite2p.gui.masks.make_buttons(parent, b0)

color buttons at row b0

suite2p.gui.masks.make_chosen_ROI(M0, ypix, xpix, v)

suite2p.gui.masks.make_chosen_circle(M0, ycirc, xcirc, col, sat)

suite2p.gui.masks.make_colorbar(parent, b0)

suite2p.gui.masks.make_colors(parent)

suite2p.gui.masks.plot_colorbar(parent)

suite2p.gui.masks.plot_masks(parent, M)

suite2p.gui.masks.rastermap_masks(parent)

suite2p.gui.masks.redraw_masks(parent, ypix, xpix)

redraw masks after roi added/removed

suite2p.gui.masks.remove_roi(parent, n, i0)

removes roi n from view i0

suite2p.gui.masks.rgb_masks(parent, col, c)

suite2p.gui.menus module

suite2p.gui.menus.classifier(parent)

suite2p.gui.menus.mainmenu(parent)

suite2p.gui.menus.manual_label(parent)

suite2p.gui.menus.mergebar(parent)

suite2p.gui.menus.plugins(parent)

suite2p.gui.menus.regPC_window(parent)

suite2p.gui.menus.reg_window(parent)

suite2p.gui.menus.registration(parent)

suite2p.gui.menus.run_suite2p(parent)

suite2p.gui.menus.suggest_merge(parent)

suite2p.gui.menus.vis_window(parent)

suite2p.gui.menus.visualizations(parent)

suite2p.gui.merge module

class suite2p.gui.merge.LineEdit(key, parent=None)

Bases: PyQt5.QtWidgets.QLineEdit

get_text()

set_text(ops)

class suite2p.gui.merge.MergeWindow(parent=None)

Bases: PyQt5.QtWidgets.QDialog

compute_merge_list(parent)

do_merge(parent)

set_merge_list(parent, goodind)

suggest_merge(parent)

suite2p.gui.merge.apply(parent)

suite2p.gui.merge.distance_matrix(parent, ilist)

suite2p.gui.merge.do_merge(parent)

suite2p.gui.merge.merge_activity_masks(parent)

suite2p.gui.reggui module

class suite2p.gui.reggui.BinaryPlayer(parent=None)

Bases: PyQt5.QtWidgets.QMainWindow

add_masks()

add_raw()

add_red()

add_zstack()

cell_chosen()

cell_mask()

compute_z(parent)

createButtons(parent)

fitToWindow()

go_to_frame()

jump_to_frame()

keyPressEvent(self, QKeyEvent)

load_zstack()

make_masks()

next_frame()

number_chosen()

open()

openCombined(save_folder)

openFile(filename, fromgui)

open_combined()

pause()

plot_clicked(event)

plot_trace()

plot_zcorr()

setup_views()

start()

updateButtons()

updateFrameSlider()

zoom_image()

class suite2p.gui.reggui.PCViewer(parent=None)

Bases: PyQt5.QtWidgets.QMainWindow

createButtons()

keyPressEvent(self, QKeyEvent)

next_frame()

open()

openFile(filename)

pause()

plot_clicked(event)

plot_frame()

start()

zoom_plot()

suite2p.gui.reggui.subsample_frames(ops, nsamps, reg_loc)

suite2p.gui.rungui module

class suite2p.gui.rungui.LineEdit(k, key, parent=None)

Bases: PyQt5.QtWidgets.QLineEdit

get_text(intkeys, boolkeys)

set_text(ops)

class suite2p.gui.rungui.OpsButton(bid, Text, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

press(parent, bid)

class suite2p.gui.rungui.RunWindow(parent=None)

Bases: PyQt5.QtWidgets.QDialog

add_batch()

add_ops()

bin_folder()

clean_script()

compile_ops_db()

create_buttons()

finished()

finished(self, int) [signal]

get_folders()

get_h5py()

load_db()

load_ops(name=None)

parse_inputformat()

remove_ops()

reset_ops()

revert_default_ops()

run_S2P()

save_default_ops()

save_folder()

save_ops()

save_text()

started()

stderr_write()

stdout_write()

stop()

class suite2p.gui.rungui.TextChooser(parent=None)

Bases: PyQt5.QtWidgets.QDialog

exit_list()

class suite2p.gui.rungui.VerticalLabel(text=None)

Bases: PyQt5.QtWidgets.QWidget

paintEvent(self, QPaintEvent)

suite2p.gui.traces module

suite2p.gui.traces.collapse_scale(parent)

suite2p.gui.traces.collapse_trace(parent)

suite2p.gui.traces.deconv_on(parent)

suite2p.gui.traces.expand_scale(parent)

suite2p.gui.traces.expand_trace(parent)

suite2p.gui.traces.make_buttons(parent, b0)

suite2p.gui.traces.nc_chosen(parent)

suite2p.gui.traces.neuropil_on(parent)

suite2p.gui.traces.plot_trace(parent)

suite2p.gui.traces.traces_on(parent)

suite2p.gui.utils module

suite2p.gui.utils.boundary(ypix, xpix)

returns pixels of mask that are on the exterior of the mask

suite2p.gui.utils.circle(med, r)

returns pixels of circle with radius 1.25x radius of cell (r)

suite2p.gui.views module

class suite2p.gui.views.RangeSlider(parent=None, *args)

Bases: PyQt5.QtWidgets.QSlider

A slider for ranges.

This class provides a dual-slider for ranges, where there is a defined maximum and minimum, as is a normal slider, but instead of having a single slider value, there are 2 slider values.

This class emits the same signals as the QSlider base class, with the exception of valueChanged

Found this slider here: https://www.mail-archive.com/pyqt@riverbankcomputing.com/msg22889.html and modified it

high()

level_change()

low()

mouseMoveEvent(self, QMouseEvent)

mousePressEvent(self, QMouseEvent)

mouseReleaseEvent(self, QMouseEvent)

paintEvent(self, QPaintEvent)

setHigh(high)

setLow(low)

class suite2p.gui.views.ViewButton(bid, Text, parent=None)

Bases: PyQt5.QtWidgets.QPushButton

custom QPushButton class for quadrant plotting requires buttons to put into a QButtonGroup (parent.viewbtns)

allows only 1 button to pressed at a time

press(parent, bid)

suite2p.gui.views.init_views(parent)

make views using parent.ops

views in order:

“Q: ROIs”, “W: mean img”, “E: mean img (enhanced)”, “R: correlation map”, “T: max projection”, “Y: mean img chan2, corr”, “U: mean img chan2”,

assigns parent.views

suite2p.gui.views.make_buttons(parent)

view buttons

suite2p.gui.views.plot_views(parent)

set parent.view1 and parent.view2 image based on parent.ops_plot[‘view’]

suite2p.gui.visualize module

class suite2p.gui.visualize.NeuronSlider(parent=None)

Bases: suite2p.gui.visualize.RangeSlider

level_change()

class suite2p.gui.visualize.RangeSlider(parent=None, *args)

Bases: PyQt5.QtWidgets.QSlider

A slider for ranges.

This class provides a dual-slider for ranges, where there is a defined maximum and minimum, as is a normal slider, but instead of having a single slider value, there are 2 slider values.

This class emits the same signals as the QSlider base class, with the exception of valueChanged

Found this slider here: https://www.mail-archive.com/pyqt@riverbankcomputing.com/msg22889.html and modified it

high()

level_change()

low()

mouseMoveEvent(self, QMouseEvent)

mousePressEvent(self, QMouseEvent)

mouseReleaseEvent(self, QMouseEvent)

paintEvent(self, QPaintEvent)

setHigh(high)

setLow(low)

class suite2p.gui.visualize.SatSlider(parent=None)

Bases: suite2p.gui.visualize.RangeSlider

level_change()

class suite2p.gui.visualize.Slider(bid, parent=None)

Bases: PyQt5.QtWidgets.QSlider

level_change(parent, bid)

class suite2p.gui.visualize.VerticalLabel(text=None)

Bases: PyQt5.QtWidgets.QWidget

paintEvent(self, QPaintEvent)

class suite2p.gui.visualize.VisWindow(parent=None)

Bases: PyQt5.QtWidgets.QMainWindow

LINE_position()

PC_on(plot)

PCreturn()

ROI_position()

THRES_position()

activate()

compute_map()

finished()

keyPressEvent(self, QKeyEvent)

neural_sorting(i)

plot_clicked(event)

plot_traces()

roi_range(roi)

select_cells()

sort_time()

stderr_write()

stdout_write()

Module contents