diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/.name b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/.name
new file mode 100644
index 0000000..b1a300f
--- /dev/null
+++ b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/.name
@@ -0,0 +1 @@
+PnP_Video_Tester
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/PnP_Video_Tester.iml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/PnP_Video_Tester.iml
new file mode 100644
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/deployment.xml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/deployment.xml
new file mode 100644
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/dictionaries/corwinperren.xml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/dictionaries/corwinperren.xml
new file mode 100644
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--- /dev/null
+++ b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/dictionaries/corwinperren.xml
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+ pickable
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\ No newline at end of file
diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/encodings.xml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/encodings.xml
new file mode 100644
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/misc.xml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/misc.xml
new file mode 100644
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/modules.xml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/modules.xml
new file mode 100644
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/workspace.xml b/OSU SARL/Desktop Applications/PnP_Video_Tester/.idea/workspace.xml
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/Run 1.png b/OSU SARL/Desktop Applications/PnP_Video_Tester/Run 1.png
new file mode 100644
index 0000000..31f0863
Binary files /dev/null and b/OSU SARL/Desktop Applications/PnP_Video_Tester/Run 1.png differ
diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.py b/OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.py
new file mode 100644
index 0000000..d61d29d
--- /dev/null
+++ b/OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.py
@@ -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 .
+
+#####################################
+# 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
\ No newline at end of file
diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.pyc b/OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.pyc
new file mode 100644
index 0000000..a3740ac
Binary files /dev/null and b/OSU SARL/Desktop Applications/PnP_Video_Tester/VideoCore.pyc differ
diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/chorionated/chorionated.png b/OSU SARL/Desktop Applications/PnP_Video_Tester/chorionated/chorionated.png
new file mode 100644
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diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/main.py b/OSU SARL/Desktop Applications/PnP_Video_Tester/main.py
new file mode 100644
index 0000000..14c3215
--- /dev/null
+++ b/OSU SARL/Desktop Applications/PnP_Video_Tester/main.py
@@ -0,0 +1,49 @@
+import sys
+from PyQt4 import QtCore, QtGui, uic
+import signal
+
+from VideoCore import PickAndPlateVideo
+
+form_class = uic.loadUiType("form.ui")[0] # Load the UI
+
+
+#####################################
+# PickAndPlateWindow Class Definition
+#####################################
+class PickAndPlateWindow(QtGui.QMainWindow, form_class):
+ def __init__(self, parent=None):
+ QtGui.QMainWindow.__init__(self, parent)
+
+ # ########## Set up QT Application Window ##########
+ 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
\ No newline at end of file
diff --git a/OSU SARL/Desktop Applications/PnP_Video_Tester/test_image.png b/OSU SARL/Desktop Applications/PnP_Video_Tester/test_image.png
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