mirror of
https://github.com/caperren/school_archives.git
synced 2025-11-09 13:41:13 +00:00
Added old video tester for using desktop to test performance of embryo blob detection algorithms
This commit is contained in:
1
OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/.name
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1
OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/.name
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PnP_Video_Tester
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11
OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/PnP_Video_Tester.iml
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11
OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/PnP_Video_Tester.iml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/deployment.xml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/deployment.xml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/encodings.xml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/encodings.xml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/misc.xml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/modules.xml
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OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/modules.xml
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868
OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/workspace.xml
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<entry file="file://$PROJECT_DIR$/VideoCore.py">
|
||||||
|
<provider selected="true" editor-type-id="text-editor">
|
||||||
|
<state relative-caret-position="0">
|
||||||
|
<caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
|
||||||
|
<folding>
|
||||||
|
<element signature="e#1199#1223#0" expanded="true" />
|
||||||
|
</folding>
|
||||||
|
</state>
|
||||||
|
</provider>
|
||||||
|
</entry>
|
||||||
|
<entry file="file://$PROJECT_DIR$/main.py">
|
||||||
|
<provider selected="true" editor-type-id="text-editor">
|
||||||
|
<state relative-caret-position="0">
|
||||||
|
<caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
|
||||||
|
</state>
|
||||||
|
</provider>
|
||||||
|
</entry>
|
||||||
|
<entry file="file://$PROJECT_DIR$/main.py">
|
||||||
|
<provider selected="true" editor-type-id="text-editor">
|
||||||
|
<state relative-caret-position="748">
|
||||||
|
<caret line="48" column="55" selection-start-line="48" selection-start-column="55" selection-end-line="48" selection-end-column="55" />
|
||||||
|
<folding />
|
||||||
|
</state>
|
||||||
|
</provider>
|
||||||
|
</entry>
|
||||||
|
<entry file="file://$PROJECT_DIR$/VideoCore.py">
|
||||||
|
<provider selected="true" editor-type-id="text-editor">
|
||||||
|
<state relative-caret-position="17">
|
||||||
|
<caret line="73" column="58" selection-start-line="73" selection-start-column="58" selection-end-line="73" selection-end-column="58" />
|
||||||
|
<folding>
|
||||||
|
<element signature="e#1199#1223#0" expanded="true" />
|
||||||
|
</folding>
|
||||||
|
</state>
|
||||||
|
</provider>
|
||||||
|
</entry>
|
||||||
|
</component>
|
||||||
|
</project>
|
||||||
BIN
OSU SARL/Desktop Applications/PnP_Video_Tester/Run 1.png
Normal file
BIN
OSU SARL/Desktop Applications/PnP_Video_Tester/Run 1.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 2.1 MiB |
289
OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.py
Normal file
289
OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.py
Normal file
@@ -0,0 +1,289 @@
|
|||||||
|
"""
|
||||||
|
This file contains the PickAndPlateVideo sub-class as part of the Framework Class
|
||||||
|
This class handles initializing and interfacing with the
|
||||||
|
"""
|
||||||
|
|
||||||
|
__author__ = "Corwin Perren"
|
||||||
|
__copyright__ = "None"
|
||||||
|
__credits__ = [""]
|
||||||
|
__license__ = "GPL (GNU General Public License)"
|
||||||
|
__version__ = "0.1 Alpha"
|
||||||
|
__maintainer__ = "Corwin Perren"
|
||||||
|
__email__ = "caperren@caperren.com"
|
||||||
|
__status__ = "Development"
|
||||||
|
|
||||||
|
# This file is part of "Pick And Plate".
|
||||||
|
#
|
||||||
|
# "Pick And Plate" is free software: you can redistribute it and/or modify
|
||||||
|
# it under the terms of the GNU General Public License as published by
|
||||||
|
# the Free Software Foundation, either version 3 of the License, or
|
||||||
|
# (at your option) any later version.
|
||||||
|
#
|
||||||
|
# "Pick And Plate" is distributed in the hope that it will be useful,
|
||||||
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
# GNU General Public License for more details.
|
||||||
|
#
|
||||||
|
# You should have received a copy of the GNU General Public License
|
||||||
|
# along with "Pick And Plate". If not, see <http://www.gnu.org/licenses/>.
|
||||||
|
|
||||||
|
#####################################
|
||||||
|
# Imports
|
||||||
|
#####################################
|
||||||
|
# Python native imports
|
||||||
|
from PyQt4 import QtCore
|
||||||
|
import cv2
|
||||||
|
import numpy
|
||||||
|
import qimage2ndarray
|
||||||
|
from math import isnan, pow, sqrt
|
||||||
|
from datetime import datetime
|
||||||
|
|
||||||
|
|
||||||
|
class PickAndPlateVideo(QtCore.QThread):
|
||||||
|
|
||||||
|
requested_image_ready_signal = QtCore.pyqtSignal()
|
||||||
|
|
||||||
|
number_embryos_detected_signal = QtCore.pyqtSignal(int, int, int)
|
||||||
|
|
||||||
|
def __init__(self, main_window):
|
||||||
|
QtCore.QThread.__init__(self)
|
||||||
|
|
||||||
|
# ########## Reference to highest level window ##########
|
||||||
|
self.main_window = main_window
|
||||||
|
|
||||||
|
# ########## Thread flags ##########
|
||||||
|
self.not_abort_flag = True
|
||||||
|
|
||||||
|
self.min_thresh = 0
|
||||||
|
self.x_res = 0
|
||||||
|
self.y_res = 0
|
||||||
|
self.x_center = 0
|
||||||
|
self.y_center = 0
|
||||||
|
self.crop_dim_half = 0
|
||||||
|
self.usable_offset = 95
|
||||||
|
|
||||||
|
self.raw_frame = None
|
||||||
|
|
||||||
|
self.images_displayed = False
|
||||||
|
|
||||||
|
self.settings_and_cal_qimage = None
|
||||||
|
self.keypoints = None
|
||||||
|
|
||||||
|
self.current_params = cv2.SimpleBlobDetector_Params()
|
||||||
|
|
||||||
|
self.raw_frame = cv2.imread('chorionated/two/chor2.png', cv2.IMREAD_COLOR)
|
||||||
|
|
||||||
|
# rows, cols, _unused = self.raw_frame.shape
|
||||||
|
#
|
||||||
|
# cv2.line(self.raw_frame, (0, rows / 2), (cols, rows / 2), (0, 255, 255), 2)
|
||||||
|
# cv2.line(self.raw_frame, (cols / 2, 0), (cols / 2, rows), (0, 255, 255), 2)
|
||||||
|
#
|
||||||
|
# rotation_matrix = cv2.getRotationMatrix2D((cols / 2, rows / 2), 2, 1)
|
||||||
|
# self.raw_frame = cv2.warpAffine(self.raw_frame, rotation_matrix, (cols, rows))
|
||||||
|
|
||||||
|
# ########## Make signal/slot connections ##########
|
||||||
|
self.connect_signals_to_slots()
|
||||||
|
|
||||||
|
# ########## Start timer ##########
|
||||||
|
self.start()
|
||||||
|
|
||||||
|
def connect_signals_to_slots(self):
|
||||||
|
pass
|
||||||
|
|
||||||
|
def run(self):
|
||||||
|
while self.not_abort_flag:
|
||||||
|
self.show_detection_calibration()
|
||||||
|
|
||||||
|
def show_detection_calibration(self):
|
||||||
|
self.setup_blob_params()
|
||||||
|
|
||||||
|
frame = cv2.cvtColor(self.raw_frame, cv2.COLOR_RGB2GRAY)
|
||||||
|
#return_val, frame = cv2.threshold(frame, self.min_thresh, 255, cv2.cv.CV_THRESH_BINARY)
|
||||||
|
|
||||||
|
mask_frame = numpy.zeros((self.y_res, self.x_res), numpy.uint8)
|
||||||
|
cv2.circle(mask_frame, (self.x_center, self.y_center), (self.crop_dim_half - self.usable_offset), 255, -1)
|
||||||
|
|
||||||
|
frame = cv2.bitwise_and(frame, mask_frame)
|
||||||
|
|
||||||
|
frame = self.masked_detect_and_overlay(frame, frame)
|
||||||
|
|
||||||
|
frame = self.crop_image(frame)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
try:
|
||||||
|
self.images_displayed = False
|
||||||
|
resized = cv2.resize(frame, (1000, 1000))
|
||||||
|
|
||||||
|
# cv2.line(resized, (0, 1000 / 2), (1000, 1000 / 2), (255, 0, 0), 1)
|
||||||
|
# cv2.line(resized, (1000 / 2, 0), (1000 / 2, 1000), (255, 0, 0), 1)
|
||||||
|
|
||||||
|
self.settings_and_cal_qimage = self.convert_to_qimage(resized)
|
||||||
|
self.requested_image_ready_signal.emit()
|
||||||
|
|
||||||
|
while not self.images_displayed:
|
||||||
|
if not self.not_abort_flag:
|
||||||
|
break
|
||||||
|
# print "Waiting"
|
||||||
|
self.msleep(10)
|
||||||
|
except:
|
||||||
|
print "Failed to convert"
|
||||||
|
|
||||||
|
def masked_detect_and_overlay(self, input_frame, overlay_frame):
|
||||||
|
detector = cv2.SimpleBlobDetector(self.current_params)
|
||||||
|
self.keypoints = detector.detect(input_frame)
|
||||||
|
#output_frame = cv2.drawKeypoints(overlay_frame, self.keypoints, color=(255, 0, 0))
|
||||||
|
|
||||||
|
# #### Test algorithm ######
|
||||||
|
detected_clean = []
|
||||||
|
valid_total = 0
|
||||||
|
pickable_total = 0
|
||||||
|
|
||||||
|
output_frame = cv2.cvtColor(overlay_frame, cv2.COLOR_GRAY2BGR)
|
||||||
|
|
||||||
|
valid_embryos = self.get_valid_embryos(self.keypoints)
|
||||||
|
pickable_embryos = self.get_pickable_embryos(valid_embryos)
|
||||||
|
|
||||||
|
output_frame = self.draw_found(output_frame, valid_embryos, pickable_embryos)
|
||||||
|
|
||||||
|
valid_total = len(valid_embryos)
|
||||||
|
pickable_total = len(pickable_embryos)
|
||||||
|
self.number_embryos_detected_signal.emit(len(self.keypoints), valid_total, pickable_total)
|
||||||
|
|
||||||
|
return output_frame
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def draw_found(frame, valid, pickable):
|
||||||
|
|
||||||
|
for embryo in valid:
|
||||||
|
cv2.circle(frame, (int(embryo[0]), int(embryo[1])), int(embryo[2]), (255, 0, 0), -1, cv2.CV_AA)
|
||||||
|
|
||||||
|
for embryo in pickable:
|
||||||
|
cv2.circle(frame, (int(embryo[0]), int(embryo[1])), int(embryo[2]), (0, 255, 0), -1, cv2.CV_AA)
|
||||||
|
|
||||||
|
return frame
|
||||||
|
|
||||||
|
def get_valid_embryos(self, keypoints):
|
||||||
|
valid = []
|
||||||
|
|
||||||
|
for point in self.keypoints:
|
||||||
|
if (not isnan(point.pt[0])) and (not isnan(point.pt[1])) and (not isnan(point.size)):
|
||||||
|
valid.append([point.pt[0], point.pt[1], point.size])
|
||||||
|
|
||||||
|
return valid
|
||||||
|
|
||||||
|
def get_pickable_embryos(self, valid):
|
||||||
|
pickable = []
|
||||||
|
min_between_embryos = self.main_window.detection_seperation_embryos_min_spin_box.value()
|
||||||
|
max_embryo_dia = self.main_window.detection_embryo_size_max_spin_box.value()
|
||||||
|
min_embryo_dia = self.main_window.detection_embryo_size_min_spin_box.value()
|
||||||
|
|
||||||
|
for embryo in valid:
|
||||||
|
x = embryo[0]
|
||||||
|
y = embryo[1]
|
||||||
|
dia = embryo[2]
|
||||||
|
|
||||||
|
if (dia >= min_embryo_dia) and (dia <= max_embryo_dia):
|
||||||
|
found_too_close = False
|
||||||
|
for comp_embryo in valid:
|
||||||
|
c_x = comp_embryo[0]
|
||||||
|
c_y = comp_embryo[1]
|
||||||
|
c_dia = comp_embryo[2]
|
||||||
|
|
||||||
|
if (x == c_x) and (y == c_y):
|
||||||
|
pass
|
||||||
|
elif (sqrt(pow(abs(x-c_x), 2) + pow(abs(y-c_y), 2))-(dia/2)-(c_dia/2)) < min_between_embryos:
|
||||||
|
found_too_close = True
|
||||||
|
break
|
||||||
|
if not found_too_close:
|
||||||
|
pickable.append(embryo)
|
||||||
|
|
||||||
|
return pickable
|
||||||
|
|
||||||
|
def setup_blob_params(self):
|
||||||
|
|
||||||
|
min_blob_dist = self.main_window.detection_min_distance_between_blobs_spin_box.value()
|
||||||
|
min_repeat = self.main_window.detection_min_repeatability_spin_box.value()
|
||||||
|
blob_thresh_min = self.main_window.detection_blob_threshold_min_spin_box.value()
|
||||||
|
blob_thresh_max = self.main_window.detection_blob_threshold_max_spin_box.value()
|
||||||
|
blob_thresh_step = self.main_window.detection_blob_threshold_step_spin_box.value()
|
||||||
|
blob_color_en = self.main_window.detection_blob_color_group_box.isChecked()
|
||||||
|
blob_color_val = self.main_window.detection_blob_color_spin_box.value()
|
||||||
|
blob_area_en = self.main_window.detection_blob_area_group_box.isChecked()
|
||||||
|
blob_area_min = self.main_window.detection_blob_area_min_spin_box.value()
|
||||||
|
blob_area_max = self.main_window.detection_blob_area_max_spin_box.value()
|
||||||
|
blob_circ_en = self.main_window.detection_blob_circularity_group_box.isChecked()
|
||||||
|
blob_circ_min = self.main_window.detection_blob_circularity_min_spin_box.value()
|
||||||
|
blob_circ_max = self.main_window.detection_blob_circularity_max_spin_box.value()
|
||||||
|
blob_conv_en = self.main_window.detection_blob_convexity_group_box.isChecked()
|
||||||
|
blob_conv_min = self.main_window.detection_blob_convexity_min_spin_box.value()
|
||||||
|
blob_conv_max = self.main_window.detection_blob_convexity_max_spin_box.value()
|
||||||
|
blob_inertia_en = self.main_window.detection_blob_inertia_group_box.isChecked()
|
||||||
|
blob_inertia_min = self.main_window.detection_blob_inertia_min_spin_box.value()
|
||||||
|
blob_inertia_max = self.main_window.detection_blob_inertia_max_spin_box.value()
|
||||||
|
|
||||||
|
self.current_params.minDistBetweenBlobs = min_blob_dist
|
||||||
|
self.current_params.minRepeatability = min_repeat
|
||||||
|
self.current_params.minThreshold = blob_thresh_min
|
||||||
|
self.current_params.maxThreshold = blob_thresh_max
|
||||||
|
self.current_params.thresholdStep = blob_thresh_step
|
||||||
|
|
||||||
|
if blob_color_en:
|
||||||
|
self.current_params.filterByColor = True
|
||||||
|
self.current_params.blobColor = blob_color_val
|
||||||
|
else:
|
||||||
|
self.current_params.filterByColor = False
|
||||||
|
|
||||||
|
if blob_area_en:
|
||||||
|
self.current_params.filterByArea = True
|
||||||
|
self.current_params.minArea = blob_area_min
|
||||||
|
self.current_params.maxArea = blob_area_max
|
||||||
|
else:
|
||||||
|
self.current_params.filterByArea = False
|
||||||
|
|
||||||
|
if blob_circ_en:
|
||||||
|
self.current_params.filterByCircularity = True
|
||||||
|
self.current_params.minCircularity = blob_circ_min
|
||||||
|
self.current_params.maxCircularity = blob_circ_max
|
||||||
|
else:
|
||||||
|
self.current_params.filterByCircularity = False
|
||||||
|
|
||||||
|
if blob_conv_en:
|
||||||
|
self.current_params.filterByConvexity = True
|
||||||
|
self.current_params.minConvexity = blob_conv_min
|
||||||
|
self.current_params.maxConvexity = blob_conv_max
|
||||||
|
else:
|
||||||
|
self.current_params.filterByConvexity = False
|
||||||
|
|
||||||
|
if blob_inertia_en:
|
||||||
|
self.current_params.filterByInertia = True
|
||||||
|
self.current_params.minInertiaRatio = blob_inertia_min
|
||||||
|
self.current_params.maxInertiaRatio = blob_inertia_max
|
||||||
|
else:
|
||||||
|
self.current_params.filterByInertia = False
|
||||||
|
|
||||||
|
self.min_thresh = self.main_window.detection_min_binary_threshold_spin_box.value()
|
||||||
|
|
||||||
|
self.x_res = 1920
|
||||||
|
self.y_res = 1080
|
||||||
|
self.x_center = 958
|
||||||
|
self.y_center = 559
|
||||||
|
self.crop_dim_half = 548/2
|
||||||
|
self.usable_offset = 83
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def convert_to_qimage(input_matrix):
|
||||||
|
return qimage2ndarray.array2qimage(input_matrix)
|
||||||
|
|
||||||
|
def crop_image(self, input_matrix):
|
||||||
|
x1 = self.x_center - self.crop_dim_half
|
||||||
|
x2 = self.x_center + self.crop_dim_half
|
||||||
|
y1 = self.y_center - self.crop_dim_half
|
||||||
|
y2 = self.y_center + self.crop_dim_half
|
||||||
|
|
||||||
|
cropped = input_matrix[y1:y2, x1:x2]
|
||||||
|
|
||||||
|
return cropped
|
||||||
|
|
||||||
|
def images_displayed_slot(self):
|
||||||
|
self.images_displayed = True
|
||||||
BIN
OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.pyc
Normal file
BIN
OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.pyc
Normal file
Binary file not shown.
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|
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|
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|
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|
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|
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|
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|
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|
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|
After Width: | Height: | Size: 1.9 MiB |
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|
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|
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|
After Width: | Height: | Size: 2.0 MiB |
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1331
OSU SARL/Desktop Applications/PnP_Video_Tester/form.ui
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1331
OSU SARL/Desktop Applications/PnP_Video_Tester/form.ui
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49
OSU SARL/Desktop Applications/PnP_Video_Tester/main.py
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49
OSU SARL/Desktop Applications/PnP_Video_Tester/main.py
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|
import sys
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from PyQt4 import QtCore, QtGui, uic
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import signal
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from VideoCore import PickAndPlateVideo
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|
form_class = uic.loadUiType("form.ui")[0] # Load the UI
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|
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|
#####################################
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# PickAndPlateWindow Class Definition
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||||||
|
#####################################
|
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class PickAndPlateWindow(QtGui.QMainWindow, form_class):
|
||||||
|
def __init__(self, parent=None):
|
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|
QtGui.QMainWindow.__init__(self, parent)
|
||||||
|
|
||||||
|
# ########## Set up QT Application Window ##########
|
||||||
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self.setupUi(self) # Has to be first call in class in order to link gui form objects
|
||||||
|
|
||||||
|
# ########## Instantiation of program classes ##########
|
||||||
|
self.video = PickAndPlateVideo(self)
|
||||||
|
|
||||||
|
self.video.requested_image_ready_signal.connect(self.on_image_ready_slot)
|
||||||
|
self.video.number_embryos_detected_signal.connect(self.on_detected_embryos_number_changed_slot)
|
||||||
|
|
||||||
|
def on_image_ready_slot(self):
|
||||||
|
try:
|
||||||
|
self.detection_calibration_image_preview_label.setPixmap(
|
||||||
|
QtGui.QPixmap.fromImage(self.video.settings_and_cal_qimage))
|
||||||
|
self.video.images_displayed = True
|
||||||
|
#print "Got here"
|
||||||
|
except:
|
||||||
|
print "Failed to show"
|
||||||
|
|
||||||
|
def on_detected_embryos_number_changed_slot(self, detected, valid, pickable):
|
||||||
|
self.detection_num_detected_label.setText(str(detected))
|
||||||
|
self.detection_valid_detected_label.setText(str(valid))
|
||||||
|
self.detection_pickable_detected_label.setText(str(pickable))
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
signal.signal(signal.SIGINT, signal.SIG_DFL) # This allows the keyboard interrupt kill to work properly
|
||||||
|
app = QtGui.QApplication(sys.argv) # Create the base qt gui application
|
||||||
|
myWindow = PickAndPlateWindow() # Make a window in this application using the pnp MyWindowClass
|
||||||
|
myWindow.show() # Show the window in the application
|
||||||
|
|
||||||
|
# screenFilter = TouchScreenEventFilter() # Still might be needed if multiple presses from touchscreen breaks stuff
|
||||||
|
# app.installEventFilter(screenFilter)
|
||||||
|
|
||||||
|
app.exec_() # Execute launching of the application
|
||||||
BIN
OSU SARL/Desktop Applications/PnP_Video_Tester/test_image.png
Normal file
BIN
OSU SARL/Desktop Applications/PnP_Video_Tester/test_image.png
Normal file
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Reference in New Issue
Block a user