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[distance_calibration] new python file containing crop and mark_checkerboard

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Xaver Roos 2022-03-28 15:30:20 +02:00
parent 5b3540e304
commit 8199fe4c7f
3 changed files with 217 additions and 12 deletions
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2
README.md
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@ -28,7 +28,7 @@ If you leave away the ```--user``` the package will be installed system-wide.
## TrackingResults
Is a class that wraps around the *.h5 files written by DeppLabCut
Is a class that wraps around the *.h5 files written by DeepLabCut
## ImageMarker

185
etrack/distance_calibration.py Normal file
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@ -0,0 +1,185 @@
from cv2 import calibrationMatrixValues
import matplotlib.pyplot as plt
import numpy as np
import cv2
import os
import sys
from IPython import embed
class DistanceCalibration:
def __init__(self, file_name, x_0=95, y_0=185, cam_dist=1.36, width=1.35, height=0.805, width_pixel=1975, height_pixel=1375, checkerboard_width=0.24, checkerboard_height=0.18,
checkerboard_width_pixel=500, checkerboard_height_pixel=350, rectangle_width=0.024, rectangle_height=0.0225, rectangle_width_pixel=100, rectangle_height_pixel=90,
rectangle_count_width=9, rectangle_count_height=7) -> None:
# aktualisieren
"""Calibration of the dimensions of the tank. Conversion of pixel into meter. Width refers to the "x-axis", height to the "y-axis" of the tank.
Args:
file_name (_type_): _description_
x_0 (int, optional): X-value of the "origin" of the tank. Defaults to 0.
y_0 (int, optional): Y-value of the "origin" of the tank. Defaults to 0.
cam_dist (int, optional): Distance of camera lense to tank floor. Defaults to 1.36.
width (int, optional): Width in meter from one lightened corner of the tank to the other. Defaults to 1.35.
heigth (int, optional): Height in meter from one lightened corner of the tank to the other. Defaults to 1.35.
width_pixel (int, optional): Width in pixel from one lightened corner of the tank to the other. Defaults to 1975.
height_pixel (int, optional): Heigth in pixel from one lightened corner of the tank to the other. Defaults to 1375.
rectangle_width (float, optional): Width of one black or corresponding white rectangle of the checkerboard. Defaults to 0.024.
rectangle_height (float, optional): Height of one black or corresponding white rectangle of the checkerboard. Defaults to 0.0225.
rectangle_count_width (int, optional): Number of black rectangles over the width of the whole checkerboard. Defaults to 9.
rectangle_count_height (int, optional): Number of black rectangles over the height of the whole checkerboard. Defaults to 7.
"""
self._file_name = file_name
self._x_0 = x_0
self._y_0 = y_0
self._width_pix = width_pixel
self._height_pix = height_pixel
self._cam_dist = cam_dist
self._width = width
self._height = height
self._cb_width = checkerboard_width
self._cb_height = checkerboard_height
self._cb_width_pix = checkerboard_width_pixel
self._cb_height_pix = checkerboard_height_pixel
self._rect_width = rectangle_width
self._rect_height = rectangle_height
self._x_factor = self.width / self.width_pix # m/pix
self._y_factor = self.height / self.height_pix # m/pix
# properties
@property
def x_0(self):
return self._x_0
@property
def y_0(self):
return self._y_0
@property
def cam_dist(self):
return self._cam_dist
@property
def width(self):
return self._width
@property
def height(self):
return self._height
@property
def width_pix(self):
return self._width_pix
@property
def height_pix(self):
return self._height_pix
@property
def x_factor(self):
return self._x_factor
@property
def y_factor(self):
return self._y_factor
def crop_movie():
if not os.path.exists(filename):
raise IOError("file %s does not exist!" % filename)
video = cv2.VideoCapture()
video.open(filename)
frame_counter = 0
success = True
frame = None
while success and frame_counter <= frame_number: # iterating until frame_counter == frame_number --> success (True)
print("Reading frame: %i" % frame_counter, end="\r")
success, frame = video.read()
frame_counter += 1
if success:
self._fig.gca().imshow(frame) # plot wanted frame of video
else:
print("Could not read frame number %i either failed to open movie or beyond maximum frame number!" % frame_number)
return []
plt.ion() # turn on interactive mode
plt.show(block=False) # block=False allows to continue interact in terminal while the figure is open
self._task_index = -1
if len(self._tasks) > 0:
self._next_task()
while not self._tasks_done:
plt.pause(0.250)
if self._interrupt:
return []
self._fig.gca().set_title("All set and done!\n Window will close in 2s")
self._fig.canvas.draw()
plt.pause(2.0)
plt.close()
return [t.marker_positions for t in self._tasks]
def mark_checkerboard(self, filename, frame_number=10):
if not os.path.exists(filename):
raise IOError("file %s does not exist!" % filename)
video = cv2.VideoCapture()
video.open(filename)
frame_counter = 0
success = True
frame = None
x_0 = self._x_0
y_0 = self._y_0
width_pix = self._width_pix
height_pix = self._height_pix
while success and frame_counter <= frame_number: # iterating until frame_counter == frame_number --> success (True)
print("Reading frame: %i" % frame_counter, end="\r")
success, frame = video.read()
frame_counter += 1
width_mean = np.mean(frame,axis=1)
crop_width_mean = width_mean[x_0:width_pix]
height_mean = np.mean(frame,axis=0)
crop_height_mean = height_mean[y_0:height_pix]
# HELLO, here you at
embed()
quit()
if success:
self._fig.gca().imshow(frame) # plot wanted frame of video
else:
print("Could not read frame number %i either failed to open movie or beyond maximum frame number!" % frame_number)
return []
plt.ion() # turn on interactive mode
plt.show(block=False) # block=False allows to continue interact in terminal while the figure is open
self._task_index = -1
if len(self._tasks) > 0:
self._next_task()
while not self._tasks_done:
plt.pause(0.250)
if self._interrupt:
return []
self._fig.gca().set_title("All set and done!\n Window will close in 2s")
self._fig.canvas.draw()
plt.pause(2.0)
plt.close()
return [t.marker_positions for t in self._tasks]
if __name__ == "__main__":
vid2 = "/home/efish/etrack/videos/2022.03.28_3.mp4"
calibration_task = DistanceCalibration(vid2)
dc = DistanceCalibration(calibration_task)
dc.mark_checkerboard(vid2, 10)
# print(sys.argv[0])
# print (sys.argv[1])
# vid1 = sys.argv[1]
embed()

42
etrack/image_marker.py
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@ -1,4 +1,6 @@
from cv2 import calibrationMatrixValues
import matplotlib.pyplot as plt
import numpy as np
import cv2
import os
import sys
@ -19,6 +21,19 @@ class ImageMarker:
self._fig.canvas.mpl_connect('key_press_event', self._key_press_event)
def mark_movie(self, filename, frame_number=0):
""" Interactive GUI to mark the corners of the tank. A specific frame of the video can be chosen. Returns marker positions.
Args:
filename: Videofile
frame_number (int, optional): Number of a frame in the videofile. Defaults to 0.
Raises:
IOError: File does not exist.
Returns:
marker_positions: Marker positions of tank corners.
"""
if not os.path.exists(filename):
raise IOError("file %s does not exist!" % filename)
video = cv2.VideoCapture()
@ -26,17 +41,17 @@ class ImageMarker:
frame_counter = 0
success = True
frame = None
while success and frame_counter <= frame_number:
while success and frame_counter <= frame_number: # iterating until frame_counter == frame_number --> success (True)
print("Reading frame: %i" % frame_counter, end="\r")
success, frame = video.read()
frame_counter += 1
if success:
self._fig.gca().imshow(frame)
self._fig.gca().imshow(frame) # plot wanted frame of video
else:
print("Could not read frame number %i either failed to open movie or beyond maximum frame number!" % frame_number)
return []
plt.ion()
plt.show(block=False)
plt.ion() # turn on interactive mode
plt.show(block=False) # block=False allows to continue interact in terminal while the figure is open
self._task_index = -1
if len(self._tasks) > 0:
@ -50,6 +65,7 @@ class ImageMarker:
self._fig.gca().set_title("All set and done!\n Window will close in 2s")
self._fig.canvas.draw()
plt.pause(2.0)
plt.close()
return [t.marker_positions for t in self._tasks]
def _key_press_event(self, event):
@ -141,11 +157,15 @@ class MarkerTask():
if __name__ == "__main__":
tank_task = MarkerTask("tank limits", ["bottom left corner", "top left corner", "top right corner", "bottom right corner"], "Mark tank corners")
feeder_task = MarkerTask("Feeder positions", list(map(str, range(1, 2))), "Mark feeder positions")
tasks = [tank_task, feeder_task]
tasks = [tank_task] # feeder_task]
im = ImageMarker(tasks)
# vid1 = "2020.12.11_lepto48DLC_resnet50_boldnessDec11shuffle1_200000_labeled.mp4"
print(sys.argv[0])
print (sys.argv[1])
vid1 = sys.argv[1]
marker_positions = im.mark_movie(vid1, 10)
print(marker_positions)
vid1 = "/home/efish/efish_tracking/efish_tracking3-Xaver-2022-03-21/videos/2022.01.12_3DLC_resnet50_efish_tracking3Mar21shuffle1_300000_labeled.mp4"
marker_positions = im.mark_movie(vid1, 100)
print(marker_positions)
# print(sys.argv[0])
# print (sys.argv[1])
# vid1 = sys.argv[1]
embed()