/
mouse_lever_tools.py
993 lines (712 loc) · 42.6 KB
/
mouse_lever_tools.py
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import glob
from PyQt4 import QtGui, QtCore
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from analysis import *
from mouse_lever import *
class MouseLeverTools(QtGui.QWidget):
def __init__(self, parent):
super(MouseLeverTools, self).__init__(parent)
self.parent = parent
layout = QtGui.QGridLayout()
#Mouse IA1 as default experiment for Greg experiments
#self.parent.root_dir = '/media/cat/12TB/in_vivo/tim/yuki/'
self.parent.root_dir = '/media/cat/12TB/in_vivo/tim/yuki/'
self.parent.replacement_dir = "12TB"# 'All.Data.3TB'
self.parent.n_sec = 3
self.parent.exp_type = 'mouse_lever'
row_index = 0 #Keep track of button/box row
self.video_rate = 15. #Video rate in Hz.
#**************************************************************************************
#******************************** SELECT ANIMAL & SESSION *****************************
#**************************************************************************************
#Select animal
self.select_lbl = QLabel('Select Experiment----->', self)
self.select_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
layout.addWidget(self.select_lbl, row_index,1)
self.comboBox_select_animal = QtGui.QComboBox(self)
file_names = sorted(glob.glob(self.parent.root_dir+"*"))
for file_name in file_names:
self.comboBox_select_animal.addItem(file_name.replace(self.parent.root_dir,''))
layout.addWidget(self.comboBox_select_animal, row_index,2)
self.comboBox_select_animal.activated[str].connect(self.select_animal); self.selected_animal = file_names[0].replace(self.parent.root_dir,'')
#Select session
self.select_lbl = QLabel('Select Session----->', self)
self.select_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
layout.addWidget(self.select_lbl, row_index,3)
self.comboBox_select_session = QtGui.QComboBox(self)
file_names = sorted(glob.glob(self.parent.root_dir + self.selected_animal + "/tif_files/*"))
for file_name in file_names:
self.comboBox_select_session.addItem(file_name.replace(self.parent.root_dir+self.selected_animal+"/tif_files/",''))
layout.addWidget(self.comboBox_select_session, row_index,4)
self.comboBox_select_session.activated[str].connect(self.select_session); self.selected_session = file_names[0].replace(self.parent.root_dir + self.selected_animal + "/tif_files/",'')
#Load Mouse from default values
self.parent.animal_name_text=self.selected_animal.replace(self.parent.root_dir,'')
self.parent.animal = Mouse_lever(self.parent.animal_name_text, self.parent.root_dir, self.parent.n_sec)
self.parent.setWindowTitle(self.parent.animal.name)
#Find movie if available:
self.movie_available_lbl = QLabel('', self)
self.movie_available_lbl.setFont(QtGui.QFont("", 12) )
if os.path.exists(self.parent.animal.home_dir+self.parent.animal.name+"/video_files/"+self.selected_session+'.m4v')==True:
self.movie_available_lbl.setText("Movie exists")
else:
self.movie_available_lbl.setText("No movie")
layout.addWidget(self.movie_available_lbl, row_index,5)
row_index+=1
#**************************************************************************************
#************************* PRE-PROCESSING BATCH / ALL SESSIONS ************************
#**************************************************************************************
self.preprocess_lbl = QLabel('PREPROCESS ALL SESSIONS', self)
self.preprocess_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
self.preprocess_lbl.setStyleSheet('color: blue')
layout.addWidget(self.preprocess_lbl, row_index, 0); row_index+=1
self.button_preprocess_mlever = QPushButton('Preprocess All Sessions')
self.button_preprocess_mlever.setMaximumWidth(200)
self.button_preprocess_mlever.clicked.connect(self.preprocess_mlever)
layout.addWidget(self.button_preprocess_mlever, row_index, 0)
self.button_filter_mlever = QPushButton('Filter All Sessions')
self.button_filter_mlever.setMaximumWidth(200)
self.button_filter_mlever.clicked.connect(self.filter_mlever)
layout.addWidget(self.button_filter_mlever, row_index, 1); row_index+=1
#**************************************************************************************
#************************* PREPROCESSING SINGLE SESSION ******************************
#**************************************************************************************
for k in range(6): layout.addWidget(QLabel(' '*40, self), row_index,k)
row_index+=1
self.preprocess_lbl = QLabel('PREPROCESS SINGLE SESSION', self)
self.preprocess_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
self.preprocess_lbl.setStyleSheet('color: blue')
layout.addWidget(self.preprocess_lbl, row_index, 0); row_index+=1
#Convert .tif to .npy
self.button1 = QPushButton('Convert .tif -> .npy')
self.button1.setMaximumWidth(200)
self.button1.clicked.connect(self.cvrt_tif_npy)
layout.addWidget(self.button1, row_index, 0)
#Align sessions
self.button1 = QPushButton('Align Sessions')
self.button1.setMaximumWidth(200)
self.button1.clicked.connect(self.algn_images)
layout.addWidget(self.button1, row_index, 1)
#Other Functions
self.button1 = QPushButton('Other Functions')
self.button1.setMaximumWidth(200)
self.button1.clicked.connect(self.algn_images)
layout.addWidget(self.button1, row_index, 2)
self.cmap = QLineEdit('viridis')
self.cmap.setMaximumWidth(50)
self.cmap_lbl = QLabel('Colour map:', self)
layout.addWidget(self.cmap_lbl, row_index,5)
layout.addWidget(self.cmap, row_index,6)
self.fps = QLineEdit('15')
self.fps.setMaximumWidth(50)
self.fps_lbl = QLabel('Video FPS:', self)
layout.addWidget(self.fps_lbl, row_index,7)
layout.addWidget(self.fps, row_index,8); row_index+=1
#************************************ FILTERING ***************************************
self.button2 = QPushButton('Pre-Filter Images')
self.button2.setMaximumWidth(200)
self.button2.clicked.connect(self.fltr_mouse_lever)
layout.addWidget(self.button2, row_index, 0)
self.filter_list = ['nofilter', 'butterworth', 'chebyshev']
self.comboBox_filter = QtGui.QComboBox(self)
for filter_ in self.filter_list[1:]: self.comboBox_filter.addItem(filter_)
layout.addWidget(self.comboBox_filter, row_index,1)
self.comboBox_filter.activated[str].connect(self.select_filter); self.selected_filter = "butterworth" #Set default
parent.filter_low = QLineEdit('0.1')
parent.filter_low.setMaximumWidth(50)
filter_low_lbl = QLabel('Low Cutoff (HZ):', self)
layout.addWidget(filter_low_lbl, row_index,2)
layout.addWidget(parent.filter_low, row_index,3)
parent.filter_high = QLineEdit('6.0')
parent.filter_high.setMaximumWidth(50)
filter_high_lbl = QLabel('High Cutoff (HZ):', self)
layout.addWidget(filter_high_lbl, row_index,4)
layout.addWidget(parent.filter_high, row_index,5)
self.n_sec_window = QLineEdit('3')
self.n_sec_window.setMaximumWidth(50)
self.n_sec_window_lbl = QLabel('Window (sec):', self)
layout.addWidget(self.n_sec_window_lbl, row_index,6)
layout.addWidget(self.n_sec_window, row_index,7)
#**************************************************************************************
#************************************ COMPUTE DFF *************************************
#**************************************************************************************
for k in range(6): layout.addWidget(QLabel(' '*40, self), row_index,k)
row_index+=1
self.preprocess_lbl = QLabel('[Ca] EVENT TRIGGERED', self)
self.preprocess_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
self.preprocess_lbl.setStyleSheet('color: blue')
layout.addWidget(self.preprocess_lbl, row_index, 0); row_index+=1
self.button3 = QPushButton('Compute DFF Pipe ====>')
self.button3.setMaximumWidth(200)
self.button3.clicked.connect(self.dff_mouse_lever)
layout.addWidget(self.button3, row_index, 0)
#Filter dropdown box
self.comboBox_select_dff_filter = QtGui.QComboBox(self)
for filter_ in self.filter_list: self.comboBox_select_dff_filter.addItem(filter_)
layout.addWidget(self.comboBox_select_dff_filter, row_index,1)
self.comboBox_select_dff_filter.activated[str].connect(self.select_dff_filter); self.selected_dff_filter = "nofilter" #Set default
#DFF method dropdown box
dff_list = ['globalAverage', 'slidingWindow']
self.comboBox_select_dff_method = QtGui.QComboBox(self)
for dff_ in dff_list: self.comboBox_select_dff_method.addItem(dff_)
layout.addWidget(self.comboBox_select_dff_method, row_index,2)
self.comboBox_select_dff_method.activated[str].connect(self.select_dff_method); self.dff_method = "globalAverage"
#Reward code dropdown box
self.locs_44threshold = []; self.code_44threshold = []
temp_file = self.parent.root_dir+self.selected_animal + '/tif_files/'+self.selected_session+'/'+self.selected_session
print temp_file
if os.path.exists(temp_file + '_locs44threshold.npy')==True:
self.locs_44threshold = np.load(temp_file+'_locs44threshold.npy')
self.code_44threshold = np.load(temp_file+'_code44threshold.npy')
self.selected_code = '02'; self.n_codes = np.count_nonzero(self.code_44threshold == self.selected_code)
#Make reward code box; May need to redo below if adding other types of codes;
self.code_list = ['02', '04', '07']
#Search for behavioural annotation data:
self.code_list.extend(self.find_annotated_clusters())
self.comboBox_select_code = QtGui.QComboBox(self)
for code_ in self.code_list:
self.comboBox_select_code.addItem(code_)
layout.addWidget(self.comboBox_select_code, row_index, 3)
self.comboBox_select_code.activated[str].connect(self.select_reward_code);
# Number of trials for reward code
self.n_codes_lbl = QLabel(str(self.n_codes), self)
layout.addWidget(self.n_codes_lbl, row_index, 4)
#Display location of trials
self.loc_trials = QPushButton('Trial Locations')
self.loc_trials.setMaximumWidth(200)
self.loc_trials.clicked.connect(self.view_trial_locations)
layout.addWidget(self.loc_trials, row_index, 5)
#Display location of trials
self.annotated_movies = QPushButton('Annotated Movies')
self.annotated_movies.setMaximumWidth(200)
self.annotated_movies.clicked.connect(self.make_annotated_movies)
layout.addWidget(self.annotated_movies, row_index, 6)
#Display location of trials
self.isolated_behaviours = QPushButton('Isolated Behaviours')
self.isolated_behaviours.setMaximumWidth(200)
self.isolated_behaviours.clicked.connect(self.find_isolated_behaviours)
layout.addWidget(self.isolated_behaviours, row_index, 7); row_index+=1
#**************************************************************************************
#************************************ VIEW DFF *************************************
#**************************************************************************************
self.button31 = QPushButton('Static STM - Single')
self.button31.setMaximumWidth(200)
self.button31.clicked.connect(self.static_stm_mouse_lever)
layout.addWidget(self.button31, row_index, 0)
self.button32 = QPushButton('Video STM')
self.button32.setMaximumWidth(200)
self.button32.clicked.connect(self.video_stm_mouse_lever)
layout.addWidget(self.button32, row_index, 1)
trial_lbl = QLabel('Select Trial:', self)
layout.addWidget(trial_lbl, row_index,2)
self.comboBox_select_trial = QtGui.QComboBox(self)
n_trials_in = self.load_trials()
self.selected_trial = ''
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #Redundant method
layout.addWidget(self.comboBox_select_trial, row_index,3)
self.comboBox_select_trial.activated[str].connect(self.initialize_trial)
self.block_save = QLineEdit('1')
self.block_save.setMaximumWidth(50)
self.block_save_lbl = QLabel('Block Ave:', self)
layout.addWidget(self.block_save_lbl, row_index,4)
layout.addWidget(self.block_save, row_index,5)
self.midline_mask = QLineEdit('1')
self.midline_mask.setMaximumWidth(50)
self.midline_mask_lbl = QLabel('MidlineMask:', self)
layout.addWidget(self.midline_mask_lbl, row_index,6)
layout.addWidget(self.midline_mask, row_index,7)
self.stm_start_time = QLineEdit('-.3')
self.stm_start_time.setMaximumWidth(50)
self.stm_start_time_lbl = QLabel('Start time:', self)
layout.addWidget(self.stm_start_time_lbl, row_index,8)
layout.addWidget(self.stm_start_time, row_index,9)
self.stm_end_time = QLineEdit('+.3')
self.stm_end_time.setMaximumWidth(50)
self.stm_end_time_lbl = QLabel('End time:', self)
layout.addWidget(self.stm_end_time_lbl, row_index,10)
layout.addWidget(self.stm_end_time, row_index,11); row_index+=1
self.static_stm_all = QPushButton('Static STM - All')
self.static_stm_all.setMaximumWidth(200)
self.static_stm_all.clicked.connect(self.static_stm_all_lever)
layout.addWidget(self.static_stm_all, row_index, 0)
self.vid_stm_all = QPushButton('Video STM - All')
self.vid_stm_all.setMaximumWidth(200)
self.vid_stm_all.clicked.connect(self.video_stm_all)
layout.addWidget(self.vid_stm_all, row_index, 1)
#************************************ EVENT TRIGGERED OPTIONS ***************************************
#self.stm_activity = QPushButton('Activity Triggered STM')
#self.stm_activity.setMaximumWidth(200)
#self.stm_activity.clicked.connect(self.view_stm_activity)
#layout.addWidget(self.stm_activity, row_index, 0)
self.mask_width = QLineEdit('12')
self.mask_width.setMaximumWidth(50)
self.mask_width_lbl = QLabel('Mask width (pixels):', self)
layout.addWidget(self.mask_width_lbl, row_index,5)
layout.addWidget(self.mask_width, row_index,6)
self.mask_percentile = QLineEdit('99.99')
self.mask_percentile.setMaximumWidth(50)
self.mask_percentile_lbl = QLabel('Mask Percentile:', self)
layout.addWidget(self.mask_percentile_lbl, row_index,7)
layout.addWidget(self.mask_percentile, row_index,8)
self.mask_power = QLineEdit('1.2')
self.mask_power.setMaximumWidth(50)
self.mask_power_lbl = QLabel('Mask Power:', self)
layout.addWidget(self.mask_power_lbl, row_index,9)
layout.addWidget(self.mask_power, row_index,10); row_index+=1
self.mask_start_frame = QLineEdit('0')
self.mask_start_frame.setMaximumWidth(50)
self.mask_start_frame_lbl = QLabel('Mask start frame:', self)
layout.addWidget(self.mask_start_frame_lbl, row_index,5)
layout.addWidget(self.mask_start_frame, row_index,6)
self.mask_end_frame = QLineEdit('6')
self.mask_end_frame.setMaximumWidth(50)
self.mask_end_frame_lbl = QLabel('Mask end frame:', self)
layout.addWidget(self.mask_end_frame_lbl, row_index,7)
layout.addWidget(self.mask_end_frame, row_index,8)
self.sigma_smooth = QLineEdit('1')
self.sigma_smooth.setMaximumWidth(50)
self.sigma_smooth_lbl = QLabel('Smooth pixels:', self)
layout.addWidget(self.sigma_smooth_lbl, row_index,9)
layout.addWidget(self.sigma_smooth, row_index,10)
row_index+=1
#**************************************************************************************
#*********************************** VIDEO TOOLS **************************************
#**************************************************************************************
for k in range(6): layout.addWidget(QLabel(' '*40, self), row_index,k)
row_index+=1
self.vid_analysis_lbl = QLabel('VIDEO ANALYSIS', self)
self.vid_analysis_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
self.vid_analysis_lbl.setStyleSheet('color: blue')
layout.addWidget(self.vid_analysis_lbl, row_index, 0); row_index+=1
#Convert videos;
self.button4 = QPushButton('Convert: .m4v => .npy')
self.button4.setMaximumWidth(200)
self.button4.clicked.connect(self.conv_video)
layout.addWidget(self.button4, row_index, 0)
#self.comboBox_select_video = QtGui.QComboBox(self)
#layout.addWidget(self.comboBox_select_video, row_index,1)
#self.comboBox_select_video.activated[str].connect(self.select); self.choice2 = ""
self.button41 = QPushButton('Find start/end of vid')
self.button41.setMaximumWidth(200)
self.button41.clicked.connect(self.fnd_start_end)
layout.addWidget(self.button41, row_index, 1)
self.button42 = QPushButton('Plot blue_light ROI')
self.button42.setMaximumWidth(200)
self.button42.clicked.connect(self.bl_light_roi)
layout.addWidget(self.button42, row_index, 2)
self.blue_light_std = QLineEdit('1.0')
self.blue_light_std.setMaximumWidth(50)
self.blue_light_std_lbl = QLabel('std of blue light):', self)
layout.addWidget(self.blue_light_std_lbl, row_index, 3)
layout.addWidget(self.blue_light_std, row_index, 4); row_index+=1
self.button431 = QPushButton('Movies: Single-Trial + [Ca]')
self.button431.setMaximumWidth(200)
self.button431.clicked.connect(self.evt_movies_ca)
layout.addWidget(self.button431, row_index, 0)
self.button43 = QPushButton('Movies: Multi-Trial')
self.button43.setMaximumWidth(200)
self.button43.clicked.connect(self.evt_movies)
layout.addWidget(self.button43, row_index, 1)
self.n_trials_movies = QLineEdit('12')
self.n_trials_movies.setMaximumWidth(50)
self.n_trials_movies_lbl = QLabel('# of trials:', self)
layout.addWidget(self.n_trials_movies_lbl, row_index, 2)
layout.addWidget(self.n_trials_movies, row_index, 3); row_index+=1
for k in range(2):
layout.addWidget(QLabel(' '*40, self), row_index,0)
row_index+=1
##**************************************************************************************
##***************************** COMBINED [Ca] & VIDEO **********************************
##**************************************************************************************
#self.preprocess_lbl = QLabel('COMBINED [Ca] & VIDEO', self)
#self.preprocess_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
#self.preprocess_lbl.setStyleSheet('color: blue')
#layout.addWidget(self.preprocess_lbl, row_index, 0); row_index+=1
#self.button_ca_stm = QPushButton('Static [Ca] + STM')
#self.button_ca_stm.setMaximumWidth(200)
#self.button_ca_stm.clicked.connect(self.static_stm_ca_mouse_lever)
#layout.addWidget(self.button_ca_stm, row_index, 0)
#self.button_ca_stm_video = QPushButton('Video [Ca] + STM')
#self.button_ca_stm_video.setMaximumWidth(200)
#self.button_ca_stm_video.clicked.connect(self.video_stm_ca_mouse_lever)
#layout.addWidget(self.button_ca_stm_video, row_index, 1)
#row_index+=1
#**************************************************************************************
#********************************** STROKE TOOLS **************************************
#**************************************************************************************
for k in range(6): layout.addWidget(QLabel(' '*40, self), row_index,k)
row_index+=1
self.post_processing_lbl = QLabel('STROKE TOOLS', self)
self.post_processing_lbl.setFont(QtGui.QFont("Times", 12, QtGui.QFont.Bold) )
self.post_processing_lbl.setStyleSheet('color: blue')
layout.addWidget(self.post_processing_lbl, row_index, 0); row_index+=1
#Load mouse from disk
self.button5 = QPushButton('Load Mouse')
self.button5.setMaximumWidth(200)
self.button5.clicked.connect(self.load_m_lever)
layout.addWidget(self.button5, row_index, 0); row_index+=1
#Separate sessions into epoch periods
epoch_days_lbl = QLabel('Epoch days: ', self)
layout.addWidget(epoch_days_lbl, row_index, 0)
#self.button6 = QPushButton('Set Epochs (days)')
#self.button6.setMaximumWidth(200)
#self.button6.clicked.connect(self.load_m_lever)
#layout.addWidget(self.button6, row_index, 0)
pre_stroke_days = 21; post_stroke_days = 14; post_post_stroke_days = 42
parent.pre_stroke_days = QLineEdit('21');
parent.pre_stroke_days.setMaximumWidth(50)
pre_stroke_days_lbl = QLabel('# days pre_stroke:', self)
layout.addWidget(pre_stroke_days_lbl, row_index,1)
layout.addWidget(parent.pre_stroke_days, row_index,2)
parent.post_stroke_days = QLineEdit('14');
parent.post_stroke_days.setMaximumWidth(50)
post_stroke_days_lbl = QLabel('# days post_stroke:', self)
layout.addWidget(post_stroke_days_lbl, row_index,3)
layout.addWidget(parent.post_stroke_days, row_index,4)
parent.post_post_stroke_days = QLineEdit('42');
parent.post_post_stroke_days.setMaximumWidth(50)
post_post_stroke_days_lbl = QLabel('# days pp_stroke:', self)
layout.addWidget(post_post_stroke_days_lbl, row_index,5)
layout.addWidget(parent.post_post_stroke_days, row_index,6) ; row_index+=1
#Dim reduction: options
self.button7 = QPushButton('Dimension Reduction:')
self.button7.setMaximumWidth(200)
self.button7.clicked.connect(self.dim_red_mouse_lever)
layout.addWidget(self.button7, row_index, 0)
self.comboBox3 = QtGui.QComboBox(self)
self.comboBox3.addItem("PCA")
self.comboBox3.addItem("MDS")
self.comboBox3.addItem("tSNE")
self.comboBox3.addItem("tSNE Barnes-Hutt")
layout.addWidget(self.comboBox3, row_index,1); row_index+=1
self.comboBox3.activated[str].connect(self.style_choice3); self.choice3="PCA"
#KMeans: options
self.button8 = QPushButton('Kmeans:')
self.button8.setMaximumWidth(200)
self.button8.clicked.connect(self.kmeans_mouse_lever)
layout.addWidget(self.button8, row_index, 0)
parent.kmeans_clusters = QLineEdit('16');
parent.kmeans_clusters.setMaximumWidth(50)
kmeans_clusters_lbl = QLabel('# of clusters:', self)
layout.addWidget(kmeans_clusters_lbl, row_index,1)
layout.addWidget(parent.kmeans_clusters, row_index,2)
#View clusters in dim reduction space
self.button9 = QPushButton('View Clusters - 3D')
self.button9.setMaximumWidth(200)
self.button9.clicked.connect(self.clusters_plot_mouse_lever)
layout.addWidget(self.button9, row_index, 3); row_index+=1
#Select a cluster from 2D trace groupings
self.button10 = QPushButton('Select Cluster - 2D')
self.button10.setMaximumWidth(200)
self.button10.clicked.connect(self.select_cluster_mouse_lever)
layout.addWidget(self.button10, row_index, 0)
#Plot Cluster Motiff
self.button11 = QPushButton('Plot Cluster Motiff')
self.button11.setMaximumWidth(200)
self.button11.clicked.connect(self.plot_motiff_mouse_lever)
layout.addWidget(self.button11, row_index, 1); row_index+=1
#Movies - single trial
self.button12 = QPushButton('Movies - Single Trial')
self.button12.setMaximumWidth(200)
self.button12.clicked.connect(self.movies_single_mouse_lever)
layout.addWidget(self.button12, row_index, 0); row_index+=1
#1D plots
self.button13 = QPushButton('1D - Plots')
self.button13.setMaximumWidth(200)
self.button13.clicked.connect(self.plot_1D_mouse_lever)
layout.addWidget(self.button13, row_index, 0)
#Pixel plots
self.button14 = QPushButton('Pixel - Plots')
self.button14.setMaximumWidth(200)
self.button14.clicked.connect(self.plot_pixel_mouse_lever)
layout.addWidget(self.button14, row_index, 1)
#Make Movies
self.button15 = QPushButton('Make Movies')
self.button15.setMaximumWidth(200)
self.button15.clicked.connect(self.make_movies_mouse_lever)
layout.addWidget(self.button15, row_index, 2) ; row_index+=1
self.setLayout(layout)
#*****************************************************************************************************
#************************************* SELECT SESSIONS FUNCTIONS *************************************
#*****************************************************************************************************
#SELECT ANIMAL
def select_animal(self, text):
print "...animal: ", text
self.selected_animal=text
self.parent.animal_name_text = text
#Reload animal object
self.parent.animal = Mouse_lever(self.parent.animal_name_text, self.parent.root_dir, self.parent.n_sec)
self.parent.setWindowTitle(self.parent.animal.name)
#Reload session list and reset session box
self.comboBox_select_session.clear()
file_names = sorted(glob.glob(self.parent.root_dir+self.parent.animal.name+"/tif_files/*"))
for file_name in sorted(file_names):
self.comboBox_select_session.addItem(file_name.replace(self.parent.root_dir+self.parent.animal.name+"/tif_files/",''))
self.selected_session = file_names[0].replace(self.parent.root_dir+self.parent.animal.name+"/tif_files/",'')
self.select_session(self.selected_session)
#Reset code functions
self.comboBox_select_code.setCurrentIndex(0)
self.locs_44threshold = []; self.code_44threshold = []
temp_file = self.selected_session+'/'+self.selected_session.replace(self.parent.animal.home_dir+self.parent.animal.name+'/tif_files/','')
if os.path.exists(temp_file + '_locs44threshold.npy')==True:
self.locs_44threshold = np.load(temp_file+'_locs44threshold.npy')
self.code_44threshold = np.load(temp_file+'_code44threshold.npy')
self.select_reward_code('02') #Reset reward code to '02' for new animal load
print self.selected_animal
print self.selected_session
print self.selected_code
#Reset trial value
n_trials_in = self.load_trials()
self.comboBox_select_trial.clear()
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #crappy method; redundant
#Find movie availabliltiy
if os.path.exists(self.parent.animal.home_dir+self.parent.animal.name+"/video_files/"+self.selected_session+'.m4v')==True:
self.movie_available_lbl.setText("Movie exists")
else:
self.movie_available_lbl.setText("No movie")
#SELECT SESSION
def select_session(self, text):
print "...session: ", text
self.selected_session=text
self.parent.animal.recName = text; self.parent.rec_name_text= text
print "... self.selected_animal: ", self.selected_animal
print "... self.selected_session: ", self.selected_session
#CALL CODE COUNTING FUNCTIONS
self.locs_44threshold = []; self.code_44threshold = []
self.tif_file = self.parent.root_dir+self.parent.animal.name+"/tif_files/" +self.selected_session+'/'+self.selected_session+'.tif'
if os.path.exists(self.tif_file[:-4] + '_locs44threshold.npy')==True:
self.locs_44threshold = np.load(self.tif_file[:-4]+'_locs44threshold.npy')
self.code_44threshold = np.load(self.tif_file[:-4]+'_code44threshold.npy')
print "... code_44threshold: ", self.code_44threshold
#Update code list values
self.code_list = ['02', '04', '07']
self.code_list.extend(self.find_annotated_clusters())
print "...updated code_list: ", self.code_list
self.comboBox_select_code.clear()
for code_ in self.code_list:
self.comboBox_select_code.addItem(code_)
self.comboBox_select_code.setCurrentIndex(0)
self.selected_code = '02'
self.n_codes = np.count_nonzero(self.code_44threshold == self.selected_code)
self.n_codes_lbl.setText(str(self.n_codes))
#Reset trial value
n_trials_in = self.load_trials()
self.comboBox_select_trial.clear()
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #crappy method; redundant
#Find movie availability
if os.path.exists(self.parent.animal.home_dir+self.parent.animal.name+"/video_files/"+self.selected_session+'.m4v')==True:
self.movie_available_lbl.setText("Movie exists")
else:
self.movie_available_lbl.setText("No movie")
#SELECT REWARD CODE
def select_reward_code(self, text):
print "...code selected: ", text
self.selected_code = text
#Load Standard Reward Codes
if (self.selected_code=='02') or (self.selected_code=='04') or (self.selected_code=='07'):
self.locs_44threshold = []; self.code_44threshold = []
temp_file = self.parent.root_dir + self.parent.animal.name + "/tif_files/"+ self.selected_session+'/'+self.selected_session
print "...temp_file: ", temp_file
if os.path.exists(temp_file + '_locs44threshold.npy')==True:
self.locs_44threshold = np.load(temp_file+'_locs44threshold.npy')
self.code_44threshold = np.load(temp_file+'_code44threshold.npy')
print self.code_44threshold
self.n_codes = np.count_nonzero(self.code_44threshold == self.selected_code)
self.n_codes_lbl.setText(str(self.n_codes))
#Load Times for specific behaviours using video annotation
else:
load_behavioural_annotation_data(self)
self.n_codes = len(self.code_44threshold_selected)
self.n_codes_lbl.setText(str(self.n_codes))
print "..reseting reward code, # codes: ", self.n_codes
print "\n\n"
#Reset trial value
n_trials_in = self.load_trials()
self.comboBox_select_trial.clear()
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #crappy method; redundant
#Initialize Trial - ONLY USED ONCE
def initialize_trial(self, text):
print "...selecting trial: ", text
self.selected_trial = text
def view_trial_locations(self):
print "... displaying trial locations..."
show_trial_locations(self)
def find_isolated_behaviours(self):
print "... finding isolated behaviours..."
find_isolated(self)
def make_annotated_movies(self):
print "... making annotated movies..."
annotate_movies(self)
#*****************************************************************************************************
#************************************* PREPROCESS ALL DATA ******************************************
#*****************************************************************************************************
def preprocess_mlever(self):
#PREPROCESS ALL DATA: Load filenames, sessions, etc.
self.parent.animal.preprocess_mouse_lever()
def filter_mlever(self):
#FILTER ALL DATA
file_names = sorted(glob.glob(self.parent.root_dir+self.parent.animal.name+"/tif_files/*"))
for file_name in sorted(file_names):
#print file_name.replace(self.parent.root_dir+self.parent.animal.name+"/tif_files/",'')
self.selected_session = file_name.replace(self.parent.root_dir+self.parent.animal.name+"/tif_files/",'')
self.select_session(self.selected_session)
filter_data(self)
def algn_images(self):
#ALIGN ALL IMAGES
file_names = sorted(glob.glob(self.parent.root_dir+self.parent.animal.name+"/tif_files/*"))
for file_name in sorted(file_names):
print file_name.replace(self.parent.root_dir+self.parent.animal.name+"/tif_files/",'')
self.selected_session = file_name.replace(self.parent.root_dir+self.parent.animal.name+"/tif_files/",'')
self.select_session(self.selected_session)
self.animal.sessfilter_data(self)
self.align_images() #Align raw_images to first session frame 1000
#load specific session .npy images and align to 1000 frame of 1st session
print "... alligning session ... NOT CURRENTLY IMPLEMENTED..."
def load_m_lever(self):
self.parent.animal.load()
#*****************************************************************************************************
#************************************* PROCESS INDIVIDUAL SESSION ************************************
#*****************************************************************************************************
def dff_mouse_lever(self):
compute_dff_mouse_lever(self)
#self.parent.animal.process_sessions(self)
#Reset trial value
n_trials_in = self.load_trials()
self.comboBox_select_trial.clear()
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #crappy method; redundant
def cvrt_tif_npy(self):
print "...convert .tif to .npy..."
#Check to see if .npy or _aligned.npy file exists
if (os.path.exists(self.tif_file[:-4] +'.npy')==False) and (os.path.exists(self.tif_file[:-4] +'_aligned.npy')==False):
print "...read: ", self.tif_file
images_raw = tiff.imread(self.tif_file)
print "... saving .npy"
np.save(self.tif_file[:-4], images_raw)
else:
print "... .npy file exists ..."
def fltr_mouse_lever(self):
filter_data(self)
def movie_available(self, text):
self.comboBox_movie_available = QtGui.QComboBox(self)
if os.path.exists(self.parent.animal.home_dir+self.parent.animal.name+"/video_files/"+self.selected_session+'.m4v')==True:
self.comboBox_movie_available.addItem("Movie exists")
else:
self.comboBox_movie_available.addItem("No movie")
layout.addWidget(self.comboBox_movie_available, row_index,5)
self.comboBox_select_session.activated[str].connect(self.movie_available)
def load_trials(self):
if self.selected_dff_filter == 'nofilter':
self.traces_filename = self.parent.animal.home_dir+self.parent.animal.name+'/tif_files/'+self.selected_session+'/'+self.selected_session+"_"+ \
str(self.parent.n_sec)+"sec_"+ self.selected_dff_filter+'_' +self.dff_method+'_'+str(self.selected_code)+"code_traces.npy"
else:
self.traces_filename = self.parent.animal.home_dir+self.parent.animal.name+'/tif_files/'+self.selected_session+'/'+self.selected_session+"_"+ \
str(self.parent.n_sec)+"sec_" + self.selected_dff_filter + "_"+self.dff_method+'_'+self.parent.filter_low.text()+"hz_"+self.parent.filter_high.text()+"hz_"+str(self.selected_code)+"code_traces.npy"
filename = self.traces_filename.replace('_traces.npy','')+'_stm.npy'
#Load trial file if data has been computed.
if os.path.exists(filename)==True:
data = np.load(filename, mmap_mode='r+')
print data.shape
return data.shape[0]
return 0
def select_dff_filter(self,text):
self.selected_dff_filter=text
#Reset trial value
n_trials_in = self.load_trials()
self.comboBox_select_trial.clear()
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #crappy method; redundant
def select_filter(self, text):
self.selected_filter = text
def select_dff_method(self, text):
self.dff_method = text
#Reset trial value
n_trials_in = self.load_trials()
self.comboBox_select_trial.clear()
for k in range(n_trials_in):
self.comboBox_select_trial.addItem(str(k))
self.selected_trial = '0' #crappy method; redundant
def find_annotated_clusters(self):
''' Find all annotation fiels called "*_clusters.npz" and add their annotations '''
filenames = glob.glob(self.parent.root_dir + self.parent.animal.name + '/tif_files/'+self.selected_session+'/'+self.selected_session+"*_clusters.npz")
self.annotated_clusters = []
for k in range(len(filenames)):
print filenames[k]
data = np.load(filenames[k])
for cluster in data['cluster_names']:
if "no_" in cluster: pass #Ignore the non-behaviour labels containing string "no_" in them.
else: self.annotated_clusters.append(cluster)
return self.annotated_clusters
#*************************************************************************************************************************************************************************
#*************************************************************************************************************************************************************************
#*************************************************************************************************************************************************************************
#*************************************************************************************************************************************************************************
#*************************************************************************************************************************************************************************
#*************************************************************************************************************************************************************************
def static_stm_mouse_lever(self):
view_static_stm(self)
def static_stm_all_lever(self):
make_static_stm_all(self)
def video_stm_mouse_lever(self):
view_video_stm(self)
def video_stm_all(self):
view_video_stm_all(self)
def style_choice2(self, text):
self.choice2 = text
def style_choice3(self, text):
self.choice3 = text
#*************************************************************************************************
#*********************************** VIDEO PROCESSING TOOLS **************************************
#*************************************************************************************************
def conv_video(self):
convert_video(self)
def fnd_start_end(self):
find_start_end(self)
def bl_light_roi(self):
plot_blue_light_roi(self)
def evt_movies(self):
event_triggered_movies_multitrial(self)
def evt_movies_ca(self):
event_triggered_movies_single_Ca(self)
#*************************************************************************************************
#****************************************** STROKE TOOLS *****************************************
#*************************************************************************************************
def kmeans_mouse_lever(self):
print "...kmeans..."
def clusters_plot_mouse_lever(self):
print "... visualizing clustered distributions in 3D post dim-reduction..."
plot_pyqt(app, dim_red_data, mouse.cluster_labels)
def select_cluster_mouse_lever(self):
print "... selecting cluster post dim-reduction..."
plot_traces_pyqt(app, mouse)
def plot_motiff_mouse_lever(self):
print "... plotting mouse lever motiff ..."
plot_selected_cluster_DFF(mouse)
def plot_1D_mouse_lever(self):
print "... plotting 1D ..."
plot_1D(mouse, generic_mask_indexes)
def plot_pixel_mouse_lever(self):
print "... plotting 1D ..."
pixel_plot(mouse, generic_mask_indexes)
def make_movies_mouse_lever(self):
print "... make movies ..."
make_movies(mouse, stacks, v_max, v_min)
def movies_single_mouse_lever(self):
print "... make movies signle trial ..."
make_movies_singletrials(mouse, data_chunks)
def dim_red_mouse_lever(self):
print "... dim reduction..."
dim_reduction (self.parent.animal, text)
def chunk_mouse_lever(self):
#Call chunking algorithm
self.parent.animal.chunk_data(pre_stroke_days, post_stroke_days, post_post_stroke_days)