Modified eyelink format bridge

Author: titoghose

PyTrack/Stimulus.py

@@ -762,8 +762,6 @@ def findMicrosaccades(self, sampling_freq=1000, plot_ms=False):
 
 		for fix_ind in range(len(fixation_indices["start"])):
 
-
-
 			all_MS = {"left" : None, "right" : None}
 			ms_count = {"left" : None, "right" : None}
 			ms_duration = {"left" : None, "right" : None}
@@ -805,9 +803,11 @@ def findMicrosaccades(self, sampling_freq=1000, plot_ms=False):
 				a1.plot(smooth_gaze["left"]["x"][1:], smooth_gaze["left"]["y"][1:])
 				a1.set_xlabel("x")
 				a1.set_ylabel("y")
-				a1.set_title("gaze plot")
+				a1.set_title("Gaze Plot	")
 				for i in range(MS["NB"]):
 					a1.plot(smooth_gaze["left"]["x"][int(MS["bin"][i][0]) : int(MS["bin"][i][1]) + 1], smooth_gaze["left"]["y"][int(MS["bin"][i][0]) : int(MS["bin"][i][1]) + 1], color='r')
+				# a1.set_xlim([-0.35, 0.25])
+				# a1.set_ylim([-0.2, 1.25])
 
 				e = Ellipse((0, 0), 2*MS["bin"][0][7], 2*MS["bin"][0][8], linestyle='--', color='g', fill=False)
 				a2.add_patch(e)
@@ -816,10 +816,11 @@ def findMicrosaccades(self, sampling_freq=1000, plot_ms=False):
 				a2.plot(vel["left"]["x"], vel["left"]["y"], alpha=0.5)
 				a2.set_xlabel("vel-x")
 				a2.set_ylabel("vel-y")
-				a2.set_title("gaze velocity plot")
+				a2.set_title("Gaze Velocity Plot")
 				for i in range(MS["NB"]):
 					a2.plot(vel["left"]["x"][int(MS["bin"][i][0]) : int(MS["bin"][i][1]) + 1], vel["left"]["y"][int(MS["bin"][i][0]) : int(MS["bin"][i][1]) + 1], color='r')
-
+				# a2.set_xlim([-25, 40])
+				# a2.set_ylim([-65, 70])
 
 				if not os.path.isdir(self.path + "/Subjects/" + self.subject_name + "/ms_gaze_vel/"):
 					os.makedirs(self.path + "/Subjects/" + self.subject_name + "/ms_gaze_vel/")
@@ -1088,7 +1089,7 @@ def findBlinkParams(self):
 		return tuple(inside_aoi)
 
 
-	def gazePlot(self, save_fig=False, show_fig=True):
+	def gazePlot(self, save_fig=False, show_fig=True, save_data=False):
 		"""Function to plot eye gaze with numbered fixations.
 
 		Internal function of class that uses its `data` member variable. Can be invoked by an object of the class.
@@ -1099,6 +1100,8 @@ def gazePlot(self, save_fig=False, show_fig=True):
 			Save the gaze plot figure or not (Defaults to ``False``). If ``True``, will be saved in the Subjects folder of the experiment folder
 		show_fig : bool
 			Display the gaze plot figure or not (Defaults to ``True``).
+		save_data : bool
+			Save the data used for plotting as a csv file.
 
 		"""
 
@@ -1126,6 +1129,7 @@ def gazePlot(self, save_fig=False, show_fig=True):
 									(self.aoi_coords[3] - self.aoi_coords[1]),
 									color='r', fill=False, linestyle='--')
 			ax.add_patch(rect)
+			print(rect.get_verts())
 
 		# Circle AOI
 		elif len(self.aoi_coords) == 3:
@@ -1134,12 +1138,14 @@ def gazePlot(self, save_fig=False, show_fig=True):
 								self.aoi_coords[2],
 								color='r', fill=False, linestyle='--')
 			ax.add_patch(ellipse)
+			print(ellipse.get_verts())
 
 		# Polygon AOI
 		else:
 			xy = np.asarray(self.aoi_coords)
 			poly = Polygon(xy, color='r', fill=False, linestyle='--')
 			ax.add_patch(poly)
+			print(poly.get_verts())
 
 
 		fixation_dict = self.findFixations()
@@ -1161,11 +1167,16 @@ def gazePlot(self, save_fig=False, show_fig=True):
 		ax.plot(self.data["InterpGaze"]["left"]["x"], self.data["InterpGaze"]["left"]["y"], 'r-')
 
 		i = 0
+		exp_data = {"ind":[], "x":[], "y":[], "gaze_x":self.data["InterpGaze"]["left"]["x"], "gaze_y":self.data["InterpGaze"]["left"]["y"]}
 		for x, y in zip(fixation_gaze_x, fixation_gaze_y):
 			ax.plot(np.mean(x), np.mean(y), 'go', markersize=15, alpha=0.7)
+			exp_data["ind"].append(i)
+			exp_data["x"].append(np.mean(x))
+			exp_data["y"].append(np.mean(y))
 			ax.text(np.mean(x), np.mean(y), str(i), fontsize=10, color='w')
 			i += 1
 
+
 		ax.set_xlim(0, int(self.width))
 		ax.set_ylim(int(self.height), 0)
 
@@ -1175,10 +1186,16 @@ def gazePlot(self, save_fig=False, show_fig=True):
 		if save_fig:
 			fig.savefig(self.path + "/Subjects/" + self.subject_name + "/gaze_plot_" + self.name + ".png", dpi=300)
 
+		if save_data:
+			max_len = max([len(exp_data[x]) for x in exp_data])
+			for key in exp_data:
+				exp_data[key] = np.pad(exp_data[key], (0, max_len - len(exp_data[key])), 'constant', constant_values=float('nan'))
+			pd.DataFrame().from_dict(exp_data).to_csv(self.path + "/Subjects/" + self.subject_name + "/gaze_plot_data_" + self.name + ".csv")
+
 		plt.close(fig)
 
 
-	def gazeHeatMap(self, save_fig=False, show_fig=True):
+	def gazeHeatMap(self, save_fig=False, show_fig=True, save_data=False):
 		"""Function to plot heat map of gaze.
 
 		Internal function of class that uses its `data` member variable. Can be invoked by an object of the class.
@@ -1189,6 +1206,8 @@ def gazeHeatMap(self, save_fig=False, show_fig=True):
 			Save the heat map figure or not (Defaults to ``False``). If ``True``, will be saved in the Subjects folder of the experiment folder
 		show_fig : bool
 			Display the heat map figure or not (Defaults to ``True``).
+		save_data : bool
+			Save the data used for plotting as a csv file.
 
 		"""
 
@@ -1267,11 +1286,18 @@ def gazeHeatMap(self, save_fig=False, show_fig=True):
 		plt.close(fig)
 
 
-	def visualize(self, show=True):
+	def visualize(self, show=True, save_data=False):
 		"""Function to create dynamic plot of gaze and pupil size.
 
 		Internal function of class that uses its `data` member variable. Does not take any input and can be invoked by an object of the class.
 
+		Paramaters
+		----------
+		show : bool
+			Open figure after plotting the data or not.
+		save_data : bool
+			Save the data used for plotting as a csv file.
+
 		"""
 		if self.data == None:
 			return

PyTrack/etDataReader.py

@@ -590,6 +590,8 @@ def message(msg):
 	fixation_flag = 0
 	saccade_flag = 0
 	blink_flag = 0
+	cont_flag = -1
+	last_time = 0
 
 	which_eye = ''
 	if eye == 'B':
@@ -599,14 +601,23 @@ def message(msg):
 
 	# loop through all lines
 	for line in raw:
-
+		# print(line)
 		# check if trial has already started
 		if started:
 			# only check for stop if there is one
 			if stop != None:
-				if stop in line:
-					started = False
-					trialend = True
+				if stop in line or last_time == cont_flag:
+					t = -1
+					if line[0:3] == "MSG":
+						ms = line.find(" ")
+						t = int(line[4:ms])
+
+					if trackertime[-1] < t:
+						cont_flag = t
+					else:
+						cont_flag = -1
+						started = False
+						trialend = True
 			# check for new start otherwise
 			else:
 				if (start in line) or (line == finalline):
@@ -795,6 +806,7 @@ def message(msg):
 
 				time.append(int(l[0])-starttime)
 				trackertime.append(int(l[0]))
+				last_time = int(l[0])
 
 
 	# # # # #

PyTrack/formatBridge.py

@@ -124,7 +124,9 @@ def toBase(et_type, filename, stim_list=None, start='START', stop=None, eye='B')
         del(temp_dict)
 
         i += 1
+        print("Progress: %.2f %" % ((i*100)/len(data)), end="\r")
 
+    print()
     return df
 
 

README.md

@@ -1,6 +1,6 @@
 [![Build Status](https://travis-ci.org/titoghose/PyTrack.svg?branch=master)](https://travis-ci.org/titoghose/PyTrack)
 [![codecov](https://codecov.io/gh/titoghose/PyTrack/branch/master/graph/badge.svg)](https://codecov.io/gh/titoghose/PyTrack)
-[![Documentation Status](https://readthedocs.org/projects/pytrack-ntu/badge/)](https://pytrack-ntu.readthedocs.io/en/latest/)
+[![Documentation Status](https://readthedocs.org/projects/pytrack-ntu/badge/?style=flat-square)](https://pytrack-ntu.readthedocs.io/en/latest/?badge=latest)
 
 # PyTrack
 
@@ -63,7 +63,7 @@ Please make sure that pip is for Python3 and not Python2. Python3  can be found
 **NOTE:** Python3 can be installed alongside Python2
 
 # Sample Data
-In order to test the toolkit some sample data in SMI, EyeLink and Tobii formats can be found [here](https://drive.google.com/open?id=1tWD69hurELVuVRFzizCbukWnr22RZrnp). The .txt file in the folder describes the data found. The SMI and Tobii files have been taken from [here](http://www2.hu-berlin.de/eyetracking-eeg/testdata.html).
+In order to test the toolkit some sample data in SMI, EyeLink and Tobii formats can be found [here](https://osf.io/f9mey/files/). The .txt file in the folder describes the data found. The SMI and Tobii files have been taken from [here](http://www2.hu-berlin.de/eyetracking-eeg/testdata.html).
 
 # Using PyTrack
 
@@ -370,8 +370,11 @@ This project is licensed under the GPL3 License - see the [LICENSE.txt](LICENSE.
 
 # Acknowledgments
 
+* We would like to thank [Dr. Dominique Makowski](https://dominiquemakowski.github.io/) for helping us develop this toolkit.
+
 * The formatsBridge module was adapted from the work done by [Edwin Dalmaijer](https://github.com/esdalmaijer) in [PyGazeAnalyser](https://github.com/esdalmaijer/PyGazeAnalyser/).
 
 * This work was done under the supervision of [Dr. Chng Eng Siong](http://www.ntu.edu.sg/home/aseschng/) - School of Computer Science and Engineering NTU and in collaboration with [Dr. Xu Hong](http://www.ntu.edu.sg/home/xuhong/) - School of Humanitites and Social Sciences NTU.
+
 * We extend our thanks to the **Department of Computer Science and Engineering Manipal Isntitute of Technology**[[link]](https://manipal.edu/mit/department-faculty/department-list/computer-science-and-engineering.html) and the **Department of Computer Science and Information Systems BITS Pilani, Hyderabad Campus** [[link]](https://www.bits-pilani.ac.in/hyderabad/computerscience/ComputerScience).
 

docs/Introduction.rst

@@ -85,7 +85,7 @@ Sample Data
 
 In order to test the toolkit some sample data in SMI, EyeLink and Tobii
 formats can be found
-`here <https://drive.google.com/open?id=1tWD69hurELVuVRFzizCbukWnr22RZrnp>`__.
+`here <https://osf.io/f9mey/files/>`__.
 The .txt file in the folder describes the data found. The SMI and Tobii
 files have been taken from
 `here <http://www2.hu-berlin.de/eyetracking-eeg/testdata.html>`__.

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="PyTrack-NTU",
-    version="0.0.12",
+    version="0.0.13",
     author="Upamanyu Ghose, Arvind Srinivasan",
     author_email="[email protected], [email protected]",
     description="An end-to-end python analysis toolkit for eye tracking",