general working state before stim value grouping
This commit is contained in:
alexanderott
parent
b0dfa22ef4
commit
8b10dba43b
7
.gitignore
vendored
7
.gitignore
vendored
@ -1,10 +1,17 @@
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*.dat
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/data/
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/temp/
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/figures/
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.idea/
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__pycache__/
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# Latex output files
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*.out
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*.aux
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*.log
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*.synctex.gz
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*.toc
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# other
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*.csv
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*.txt
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@ -6,7 +6,7 @@ from warnings import warn
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import matplotlib.pyplot as plt
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class DataProvider:
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class Controller:
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def __init__(self, data_path, repros_todo=(), base_detection_params=(2, 5000, 1000)):
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self.data_path = data_path
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@ -28,12 +28,31 @@ class DataProvider:
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self.repros_todo = self.repros
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self.base_detection_parameters = base_detection_params
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self.thresholds = {}
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self.sampling_interval = self.parser.get_sampling_interval()
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self.sorting = {}
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self.thresholds = {}
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self.recording_times = {}
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def save_parameters(self):
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header = "trial_index,threshold,min_window,step_size\n"
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for repro in self.thresholds.keys():
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# TODO change '.' to self.data_path after testing:
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with open("." + "/{}_thresholds.csv".format(repro), "w") as threshold_file:
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threshold_file.write(header)
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for i in range(len(self.sorting[repro])):
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if len(self.thresholds[repro][i]) == 0:
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# missing threshold info
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threshold_file.write("{},{},{},{}\n".format(i, -1, -1, -1))
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else:
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# format and write given thresholding parameters
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thresh = self.thresholds[repro][i][0]
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min_window = self.thresholds[repro][i][1]
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step = self.thresholds[repro][i][2]
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threshold_file.write("{},{},{},{}\n".format(i, thresh, min_window, step))
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print("Thresholds saved!")
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# TODO save redetected spikes:
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def get_repros(self):
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return self.parser.get_measured_repros()
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@ -94,6 +113,12 @@ class DataProvider:
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def get_trials(self, repro, stimulus_value):
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pass
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def set_redetection_params(self, repro, trial_idx, params):
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if repro not in self.thresholds.keys():
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self.thresholds[repro] = [(),]*len(self.sorting[repro])
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self.thresholds[repro][trial_idx] = params
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def calculate_distance_matrix_traces_spikes(traces, spiketimes, sampling_rate, before):
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ash = np.zeros((len(traces), len(spiketimes)))
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@ -131,7 +131,7 @@ class DatParser:
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def get_baseline_spiketimes(self):
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# TODO change: reading from file -> detect from v1 trace
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spiketimes = []
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warn("Spiketimes don't fit time-wise to the baseline traces. Causes different vector strength angle per recording.")
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# warn("Spiketimes don't fit time-wise to the baseline traces. Causes different vector strength angle per recording.")
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for metadata, key, data in Dl.iload(self.baseline_file):
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spikes = np.array(data[:, 0]) / 1000 # timestamps are saved in ms -> conversion to seconds
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@ -296,7 +296,7 @@ class DatParser:
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spiketimes = []
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metadata_list = []
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warn("get_spiketimes():Spiketimes aren't sorted the same way as traces!")
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# warn("get_spiketimes():Spiketimes aren't sorted the same way as traces!")
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if spiketimes_file == "":
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if repro not in self.spike_files.keys():
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@ -1,30 +1,29 @@
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from PyQt5.QtWidgets import QWidget, QPushButton, QSizePolicy, QLineEdit,\
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QMessageBox, QVBoxLayout, QHBoxLayout, QGridLayout, QLabel, QFrame,\
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QDoubleSpinBox, QComboBox, QSpinBox
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QDoubleSpinBox, QComboBox, QSpinBox, QCheckBox
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from PyQt5.QtCore import pyqtSlot
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import numpy as np
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from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
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from matplotlib.figure import Figure
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from DataProvider import DataProvider
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from Controller import Controller
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from redetector import detect_spiketimes
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class SpikeRedetectGui(QWidget):
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def __init__(self, data_provider: DataProvider):
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def __init__(self, controller: Controller):
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super().__init__()
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self.data_provider = data_provider
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self.controller = controller
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self.title = 'Spike Redetection'
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self.left = 10
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self.top = 10
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self.width = 640
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self.height = 400
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self.width = 1500
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self.height = 800
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self.trial_idx = 0
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self.initUI()
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def initUI(self):
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@ -35,7 +34,6 @@ class SpikeRedetectGui(QWidget):
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middle = QHBoxLayout()
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# Canvas Area for matplotlib figure
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plot_area = QFrame()
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plot_area_layout = QVBoxLayout()
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self.canvas = PlotCanvas(self)
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@ -48,26 +46,26 @@ class SpikeRedetectGui(QWidget):
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plot_area_buttons.setLayout(plot_area_buttons_layout)
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plot_area_layout.addWidget(plot_area_buttons)
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button = QPushButton('Button1', self)
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button = QPushButton('previous stimulus value', self)
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button.setToolTip('A nice button!')
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button.clicked.connect(lambda: self.threshold_spinbox.setValue(1))
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button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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plot_area_buttons_layout.addWidget(button)
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button = QPushButton('Button2', self)
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button = QPushButton('previous trial', self)
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button.setToolTip('Another nice button!')
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button.clicked.connect(lambda: self.threshold_spinbox.setValue(2))
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button.clicked.connect(lambda: self.trial_change(self.trial_idx - 1))
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button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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plot_area_buttons_layout.addWidget(button)
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button = QPushButton('Button3', self)
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button = QPushButton('next trial', self)
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button.setToolTip('Even more nice buttons!')
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button.clicked.connect(lambda: self.threshold_spinbox.setValue(3))
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button.clicked.connect(lambda: self.trial_change(self.trial_idx + 1))
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button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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plot_area_buttons_layout.addWidget(button)
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button = QPushButton('Button4', self)
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button.setToolTip('Even more nice buttons!')
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button = QPushButton('next stimulus value', self)
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button.setToolTip('But this is not a nice button!')
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button.clicked.connect(lambda: self.threshold_spinbox.setValue(4))
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button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
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plot_area_buttons_layout.addWidget(button)
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@ -85,40 +83,43 @@ class SpikeRedetectGui(QWidget):
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stim_val_label = QLabel("Stimulus value:")
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self.stim_val_box = QComboBox()
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repro_label = QLabel("Repro:")
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panel_layout.addWidget(repro_label)
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self.repro_box = QComboBox()
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for repro in self.data_provider.get_repros():
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self.repro_box.addItem(repro)
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self.repro_box = QComboBox()
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self.repro_box.addItems(self.controller.get_repros())
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self.repro_box.currentTextChanged.connect(self.repro_change)
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panel_layout.addWidget(self.repro_box)
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stim_val_label = QLabel("Stimulus value:")
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panel_layout.addWidget(stim_val_label)
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self.stim_val_box = QComboBox()
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panel_layout.addWidget(self.stim_val_box)
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trial_label = QLabel("Trial:")
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panel_layout.addWidget(trial_label)
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trial_spinbox = QSpinBox(self)
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trial_spinbox.setValue(1)
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trial_spinbox.setSingleStep(1)
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trial_spinbox.valueChanged.connect(lambda: self.trial_change(trial_spinbox.value()))
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panel_layout.addWidget(trial_spinbox)
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self.grouping_checkbox = QCheckBox()
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self.grouping_checkbox.setText("Group by Stimulus Value:")
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panel_layout.addWidget(self.grouping_checkbox)
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filler = QFill(minh=200)
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panel_layout.addWidget(filler)
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self.status_label = QLabel("Done x/15 Stimulus Values")
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panel_layout.addWidget(self.status_label)
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trial_label = QLabel("Trial:")
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panel_layout.addWidget(trial_label)
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self.trial_spinbox = QSpinBox(self)
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self.trial_spinbox.setValue(self.trial_idx)
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self.trial_spinbox.setSingleStep(1)
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self.trial_spinbox.valueChanged.connect(lambda: self.trial_change(self.trial_spinbox.value()))
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panel_layout.addWidget(self.trial_spinbox)
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# self.status_label = QLabel("Done x/15 Stimulus Values")
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# panel_layout.addWidget(self.status_label)
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filler = QFill()
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panel_layout.addWidget(filler)
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threshold_label = QLabel("Threshold:")
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panel_layout.addWidget(threshold_label)
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self.threshold_spinbox = QDoubleSpinBox(self)
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self.threshold_spinbox.setValue(self.data_provider.base_detection_parameters[0])
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self.threshold_spinbox.setValue(self.controller.base_detection_parameters[0])
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self.threshold_spinbox.setSingleStep(0.5)
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self.threshold_spinbox.valueChanged.connect(lambda: self.redetection_changed())
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panel_layout.addWidget(self.threshold_spinbox)
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@ -127,7 +128,7 @@ class SpikeRedetectGui(QWidget):
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panel_layout.addWidget(window_label)
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self.window_spinbox = QSpinBox(self)
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self.window_spinbox.setMaximum(2**21)
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self.window_spinbox.setValue(self.data_provider.base_detection_parameters[1])
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self.window_spinbox.setValue(self.controller.base_detection_parameters[1])
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self.window_spinbox.setSingleStep(500)
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self.window_spinbox.valueChanged.connect(lambda: self.redetection_changed())
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panel_layout.addWidget(self.window_spinbox)
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@ -136,43 +137,77 @@ class SpikeRedetectGui(QWidget):
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panel_layout.addWidget(step_label)
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self.step_spinbox = QSpinBox(self)
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self.step_spinbox.setMaximum(2 ** 21)
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self.step_spinbox.setValue(self.data_provider.base_detection_parameters[2])
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self.step_spinbox.setValue(self.controller.base_detection_parameters[2])
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self.step_spinbox.setSingleStep(200)
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self.step_spinbox.valueChanged.connect(lambda: self.redetection_changed())
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panel_layout.addWidget(self.step_spinbox)
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button = QPushButton('Accept!', self)
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button.setToolTip('Accept the threshold for current stimulus value')
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button.clicked.connect(self.accept_redetection)
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panel_layout.addWidget(button)
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button = QPushButton('Save thresholds!', self)
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button.setToolTip('Save accepted thresholds!')
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button.clicked.connect(self.save_threshold_parameters)
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panel_layout.addWidget(button)
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panel.setLayout(panel_layout)
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middle.addWidget(panel)
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self.setLayout(middle)
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# init the first repro:
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self.repro_change()
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self.show()
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@pyqtSlot()
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def redetection_changed(self):
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redetection = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
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self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.data_provider, redetection)
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self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.controller, redetection)
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@pyqtSlot()
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def trial_change(self, new_trial_idx):
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# TODO test if in range of trials!
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if new_trial_idx == self.trial_idx:
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return
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traces, spiketimes, recording_times = self.controller.get_traces_with_spiketimes(self.repro_box.currentText())
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if not 0 <= new_trial_idx < len(spiketimes):
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print("trial_change():Out of range trial index!")
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return
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self.trial_idx = new_trial_idx
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if new_trial_idx != self.trial_spinbox.value():
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self.trial_spinbox.setValue(new_trial_idx)
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redetection = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
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self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.data_provider, redetection)
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self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.controller, redetection)
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@pyqtSlot()
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def repro_change(self):
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repro = self.repro_box.currentText()
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# reset trials and stim values
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self.trial_change(0)
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self.stim_val_box.clear()
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for val in self.data_provider.get_stim_values(repro):
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for val in self.controller.get_stim_values(repro):
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self.stim_val_box.addItem(str(val))
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redetection = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
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self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.data_provider, redetection)
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self.canvas.plot(self.trial_idx, self.repro_box.currentText(), self.controller, redetection)
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@pyqtSlot()
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def accept_redetection(self):
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params = (self.threshold_spinbox.value(), self.window_spinbox.value(), self.step_spinbox.value())
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self.controller.set_redetection_params(self.repro_box.currentText(), self.trial_idx, params)
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self.trial_change(self.trial_idx + 1)
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@pyqtSlot()
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def save_threshold_parameters(self):
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self.controller.save_parameters()
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class PlotCanvas(FigureCanvas):
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@ -189,6 +224,7 @@ class PlotCanvas(FigureCanvas):
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QSizePolicy.Expanding)
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FigureCanvas.updateGeometry(self)
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self.current_repro = None
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self.mouse_button_pressed = False
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self.mouse_button = "-1"
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@ -249,7 +285,6 @@ class PlotCanvas(FigureCanvas):
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self.axes.set_ylim(new_ylimits)
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self.draw()
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def onclick(self, event):
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if event.button in (1, 3):
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@ -272,7 +307,7 @@ class PlotCanvas(FigureCanvas):
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self.mouse_button_pressed = False
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@pyqtSlot()
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def plot(self, trial_idx, repro, data_provider: DataProvider, redetection_vars):
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def plot(self, trial_idx, repro, data_provider: Controller, redetection_vars):
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traces, spiketimes, recording_times = data_provider.get_traces_with_spiketimes(repro)
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trace = traces[trial_idx]
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spiketimes = spiketimes[trial_idx]
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@ -289,8 +324,12 @@ class PlotCanvas(FigureCanvas):
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redetect = detect_spiketimes(time, trace, redetection_vars[0], redetection_vars[1], redetection_vars[2])
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ax.eventplot(redetect, lineoffsets=max(trace) + 2, colors="red")
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ax.set_title('Trial XYZ')
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ax.set_xlim(xlim)
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ax.set_ylim(ylim)
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if self.current_repro == repro:
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ax.set_xlim(xlim)
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ax.set_ylim(ylim)
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else:
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self.current_repro = repro
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self.draw()
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18
main.py
18
main.py
@ -1,17 +1,29 @@
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import sys
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from PyQt5.QtWidgets import QApplication
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import os
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from DataProvider import DataProvider
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from PyQt5.QtWidgets import QApplication, QFileDialog
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from Controller import Controller
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from SpikeRedetectGui import SpikeRedetectGui
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test_file = "../neuronModel/data/final_sam/2010-11-08-al-invivo-1"
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def main():
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app = QApplication(sys.argv)
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data_provider = DataProvider("../neuronModel/data/final_sam/2010-11-08-al-invivo-1")
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data_path = QFileDialog.getExistingDirectory(caption='Select a directory')
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if os.path.isdir(data_path):
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data_provider = Controller(data_path)
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else:
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print("Cell loading didn't work!\n Cell folder: {}".format(data_path))
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return
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#data_provider = Controller(test_file)
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ex = SpikeRedetectGui(data_provider)
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sys.exit(app.exec_())
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if __name__ == '__main__':
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main()
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@ -1,6 +1,6 @@
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from DatParser import DatParser
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from DataProvider import DataProvider, average_spike_height
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from Controller import Controller, average_spike_height
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import os
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import numpy as np
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@ -18,7 +18,7 @@ def main():
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if cell in failure_to_read_sam:
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continue
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cell_folder = os.path.join(DATA_FOLDER, cell)
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data_provider = DataProvider(cell_folder)
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data_provider = Controller(cell_folder)
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repros = test_getting_repros(data_provider)
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@ -42,7 +42,7 @@ def main():
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plt.close()
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def test_loading_spikes(data_provider: DataProvider, repro):
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def test_loading_spikes(data_provider: Controller, repro):
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return data_provider.parser.get_spiketimes(repro)
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@ -50,7 +50,7 @@ def test_loading_traces(data_provider, repro):
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return data_provider.get_traces(repro)
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def test_getting_repros(data_provider: DataProvider):
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def test_getting_repros(data_provider: Controller):
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return data_provider.get_repros()
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Block a user