From 8199fe4c7f17ab6a4e6bd5a6ee7d1013beddcb8d Mon Sep 17 00:00:00 2001
From: Xaver Roos <xaver.roos@gmail.com>
Date: Mon, 28 Mar 2022 15:30:20 +0200
Subject: [PATCH] [distance_calibration] new python file containing crop and
mark_checkerboard
---
README.md | 2 +-
etrack/distance_calibration.py | 185 +++++++++++++++++++++++++++++++++
etrack/image_marker.py | 42 ++++++--
3 files changed, 217 insertions(+), 12 deletions(-)
create mode 100644 etrack/distance_calibration.py
diff --git a/README.md b/README.md
index efed3c4..8e4dcec 100644
--- a/README.md
+++ b/README.md
@@ -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
diff --git a/etrack/distance_calibration.py b/etrack/distance_calibration.py
new file mode 100644
index 0000000..c859b9e
--- /dev/null
+++ b/etrack/distance_calibration.py
@@ -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()
\ No newline at end of file
diff --git a/etrack/image_marker.py b/etrack/image_marker.py
index 8ad7bad..82ca605 100644
--- a/etrack/image_marker.py
+++ b/etrack/image_marker.py
@@ -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)
\ No newline at end of file
+
+ 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()
\ No newline at end of file