gui module

Main class for setting up user interface and instantiate network connections.

opeth.gui.AUTOTRIGGER_CH = None

Set to None to disable, otherwise TTL pulses will be generated if given channel is over threshold

opeth.gui.CHANNELPLOTS_ANTIALIASED = True

More professional display for per channel plots, but less visible

opeth.gui.CHANNELPLOTS_VERTICAL_OFFSET = 0.1

When histogram are presented with lines per channel, adjust the way they are plotted.

opeth.gui.CHANNELS_PER_HISTPLOT = 4

Channels per tetrode to be combined in histogram

opeth.gui.COLUMN_INCREMENTS = [3, 8, 12, 20, 25, 30, 42, 64, 90, 110, 120, 130, 1000]

A value in a given index means maximum number of plots displayed for the index number of columns

opeth.gui.DEBUG = False

Enable or disable debug mode

opeth.gui.DEBUG_FPS = False

Enable frame per sec debug prints

opeth.gui.DEBUG_FPSREPORT_PERIOD = 5

FPS debug print update frequency

opeth.gui.DEBUG_TIMING = False

Enable timing prints

opeth.gui.DEFAULT_INI = 'default.ini'

Config file name defaults

opeth.gui.DEFAULT_SPIKE_THRESHOLD = 3e-05

Spike threshold set as default parameter if no ini file found.

class opeth.gui.GuiClass

Bases: object

Main GUI handling class.

Creates windows:

• Main histogram window with parameters.
• Raw data window with real time plotted continuous scrolling waveform for overview.
• Debug window if DEBUG is True.
• Spike analysis windows using spike_gui.SpikeEvalGui when corresponding button is pressed.

At startup as long as no data is present the histogram windows are not populated as the input data channel count is not known.

The main loop performing the most important periodic operations is in update() method, calling e.g. comm.CommProcess.timer_callback() to collect data and based on that update plot data.

rawdata_curves

Top part waveforms of raw analog window

Type:list

ttlraw_curves

Bottom part waveforms of raw analog window

Type:list

cp

Interface and data collector to OE

Type:comm.CommProcess

dataproc

Data processor instance working on cp’s colldata.Collector data

Type:colldata.DataProc

mainwin

Main window with histogram and parameter setup window

Type:QtGui.QMainWindow

rawdatawin

Real time raw analog data display with a continuously scrolling part and a TTL-aligned snapshot.

Type:pyqtgraph.GraphicsWindow

debugwin

Opened only if DEBUG is True, displays some internal variables for debugging

Type:QtGui.QWidget

spike_bin_ms

Histogram bins, one row per channel, each row contains ttl_range_ms + 1 number of bins for collecting spike offsets relative to event.

Type:2D np.ndarray

ttl_range_ms

TTL range specified by start and end value in event_roi (warning: if HISTOGRAM_BINSIZE modified, it is not ms any more!)

Type:int

event_roi

Region of interest around event ([start, end] values in second around TTL pulse for spike search region and plotting e.g. [-0.02, 0.05] for default 20 ms before, 50 ms after)

Type:list of two float elements

configfname

Name of config file for parameter setup storage. PARAMFNAME points to the file from where its initial value is read during program startup.

Type:str

threshold_levels

One row per tetrode, threshold level in uV. Same sign both for negative and positive spikes as in GUI, will be adjusted afterwards for spike detection.

Type:np.ndarray of floats

histplots

Histogram plot collection for data updates - each element is a collection of per-channel histograms for a given tetrode.

Type:list of lists of plots

MAX_PLOT_PER_SEC = 4

Perfomance limit through earliest_hist_plot

change_event_roi(new_roi, clear_plot=True, **kwargs)

Change region of interest around event (spike search range) and update plots.

clear_plot()

Clear all displayed histograms

convert_strlist_to_ints(str_in)

Convert a text entry of disabled channels to an integer list.

Parameters:str_in (str) – input string in the format 1-4, 17, 30-33. Returns:a list of integers like [1,2,3,4,17,30,31,32,33].

disabled_channels = None

A list of disabled channels starting with 0

display_brushcolors = None

Histogram colors

display_linecolors = None

Channel plot (line) colors

display_theme = None

display theme

downsampling_rate = None

Downsampling rate is calculated from sampling rate, target is 1kHz for raw data window

earliest_hist_plot = None

Next histogram update time for performance cap

earliest_rawttl_plot = None

Next raw analog TTL-aligned display time - lower window update rate limit

force_update = None

Keep track of programmatic parameter changes to prevent infinite loops.

init_debugwin()

Open a new debug window - called only if DEBUG is enabled.

init_histwin()

Initialize main histogram window and parameters with defaults.

Actual display will be updated in populate_histwin() once number of channels/channels per tetrode is known.

init_params(paramcontainer, reset=False, **kwargs)

Prepare parameter setup part of main histogram window.

init_rawwin()

Real time display of current waveform for visible feedback even when signal thresholds may be off.

init_spikewin()

Single channel analysis window

initgraph()

Called at startup to set up the main window with the parameter setup and the raw data window.

Only a placeholder text is displayed instead of histogram plots until the first set of data arrived and channel count becomes known.

load_params()

Load parameters from config file configfname

Called after file selection dialog when Load button pressed, and also when program is first loaded.

more_than_two_continuous(intlist)

In order to reduce a string of ‘1, 2, 3, 4’ to ‘1-4’ return the longest series of numbers incrementing by one at the beginning of an intlist.

Helper function for update_disabled_channels(), the opposite of convert_strlist_to_ints() (partially).

Parameters:intlist (list) – a list of integers Returns:either the first element of intlist or a list of elements if more than two consecutive numbers were incrementing by one.

onChangeTheme()

onClearPlot()

Manually clear plots on button press.

onClose(event)

Handler for closeEvent of main window (histogram window), should close all other windows before closing the main window.

onLoadParams()

onOpenSpikeWin()

Open new spike analysis window on button press.

onParamChange(param, changes)

Called on any parameter change.

onResetParams()

Remove saved parameters and reinit parameter setup. Called when corresponding button was pressed.

onSaveAsParams()

Store parameter setup in file. Called when corresponding button pressed.

onSaveParams()

populate_histwin()

Create an array of dockable/movable histograms. The layout is determined by the number of necessary plot windows and the COLUMN_INCREMENTS variable.

populate_params()

Update parameter setup after channel count is known.

populate_rawwin()

Create as many raw analog display curves as necessary based on nChannels

restore_params()

Startup code performing parameter restoration.

save_params()

Save parameters to configfname

Called when Save or Save as buttons pressed.

set_threshold_levels(value)

Parameter setup: update all the tetrode threshold level values simultaneously.

should_restore_params = None

Automatic parameter reload should happen only on startup.

store_lastconfname(fname)

Store configfname in file PARAMFNAME and update config box display to show new file name.

fname

Path to new file - if left empty then will default to DEFAULT_INI.

Type:str

timeas = None

Profiling class

timing_start = None

internal elapsed time measurement scheduler

Type:Debug

update(**kwargs)

The main loop, processes input data and updates plots. Called periodically from a Qt timer.

On very first round with actual data present it calls update_channelcnt() to create the necessary amount of histogram plots.

Periodically calls

• comm.CommProcess.timer_callback() to fetch new data
• colldata.Collector.keep_last() to drop old data
• colldata.Collector.process_ttl() to fetch region of interest around TTL
• colldata.DataProc.compress() to reduce complexity of the real time plot
• colldata.DataProc.spikedetect() to find spikes
• update spike analysis windows update_spikewins()

and updates real time plot data via rawdata_curves and ttlraw_curves

spike_bin_ms

Histogram bins containing one row per channel of spike event counter bins (accumulating); first item per row contains the bin corresponding to start of trigger area ( event_roi [0] ) and last one to the end ( event_roi [1] )

Type:2D numpy array

data_at_ttl

Each row contains the same number of samples from different channels

Type:2D numpy array

data_ts

Timestamps of data_at_ttl samples around TTL (in seconds, used for binning)

Type:1D numpy array

data_ts_0

Same array as data_ts, start offset removed (timestamp of first sample is 0), used for histogram generation (binning)

Type:1D numpy array

data_ts_roi

TTL timestamps with actual TTL event aligned to 0 (one ts for each sample - samples start earlier than TTL), used for plotting the time scale

Type:1D numpy array

spike_pos

each internal list contains sample index of spike events for a given channel (events over threshold, disabled channels not included)

Type:list of lists

spike_ts

Same layout as spike_pos, contains the actual timestamps of spikes for plotting x axis

Type:list of lists

update_cfgboxtitle()

Update config box title to show the current config file, reduce length if necessary.

update_channelcnt(nChannels)

Called when number of channels becomes known or changes.

Update the necessary display elements (number of histogram plots etc).

Parameters:nChannels (int) – number of input channels (as detected in first chunk of data received from OE)

update_disabled_channels()

Called when list of disabled channels is entered; it parses the input string to understand and abbreviate series of numbers.

Uses convert_strlist_to_ints() and reproduces the string with more_than_two_continuous() in order to verify syntax and to combine input like 1, 2, 3 to 1-3.

update_histograms()

Update displayed histogram plots.

Types of histogram plots available:

• the normal histogram with e.g. 4 channels per tetrode combined

  into a single histogram, channels indistinguishable

• same histogram but each channel with its own colour, a histogram

  bar consisting of Ch1+Ch2+Ch3+Ch4 separated by colour (same outline as in previous case just 4 colours instead of 1)

  Trick for display: 4 plots displayed, ch1 in front, ch1+ch2 aggregated behind etc.

• per channel: lines instead of bar graphs to make it possible to

  distinguish between overlapping elements

update_plotcolors()

Called when channels get disabled - no need to remove plots

update_plotstyle()

If the plot style changes from one of the histogram plots to channel plot or vica versa, the channel colors are to be updated.

update_samplingrate(sampling_rate, clear_plot=False)

update_spikewins(data_ts, data, spike_ts, spike_pos)

Perform an update on spike windows.

update_threshold_levels()

Update the internal threshold levels based on the UI parameters.

opeth.gui.HIDE_AUX_CHANNELS = True

Whether AUXiliary channels (in 35 channel case last 3 channels, in 70 channel case last 6) should be omitted.

opeth.gui.HISTOGRAM_BINSIZE = 0.001

Histogram bin size in seconds

opeth.gui.MAX_CHANNELS_PER_PLOT = 8

Maximal number of channels for a given histogram window/polytrode

opeth.gui.MAX_TRIGGER_CHANNEL = 8

TTL trigger channel is up to 8 for a BNC expansion board

opeth.gui.NEGATIVE_THRESHOLD = True

Inverted signal - positive threshold value in params mean negative threshold with falling edge detection

opeth.gui.PARAMFNAME = 'lastini.conf'

Last used ini file name stored in a file, will default to DEFAULT_INI if missing

opeth.gui.RERECORD = False

True if data is to be saved for debug purposes

opeth.gui.SPIKEWIN = False

Set to True if one spike analysis window is to be opened at start.

opeth.gui.TRIGGER_HOLDOFF = 0.001

Trigger holdoff in seconds

class opeth.gui.Theme

Bases: enum.Enum

An enumeration.

dark = 0

publication = 1

class opeth.gui.TimeMeasClass

Bases: object

Performance monitoring/profiling class. (Just for development.)

Maintains a dictionary of elapsed times and number of calls with separate identifier strings to make it possible to measure multiple overlapping time segments.

dump()

Display all timer results.

reset()

Restart all timers.

tic(idstr)

Start timer.

Parameters:idstr (str) – Starts timer for given string id. Will be terminated by toc().

timecount = None

Number of measurements collected in timespent (for averaging)

timespent = None

Measurement array for elapsed time

timestart = None

Last measurement’s start time (initialized in tic())

toc(idstr)

Stop timer, increment corresponding timer arrays.

Parameters:idstr (str) – Index string of timespent and timecount. Returns:elapsed time since last tic in seconds

opeth.gui.main()

opeth.gui.sigint_handler(*args)

Handler for the SIGINT signal in order to be able to quit pressing CTRL+C in console.