Added LS100 files

free_swimming_4fish_setup/alignment/camera_alignment.ui

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+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Dialog</class>
+ <widget class="QDialog" name="Dialog">
+  <property name="enabled">
+   <bool>true</bool>
+  </property>
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>1363</width>
+    <height>970</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Dialog</string>
+  </property>
+  <widget class="QLabel" name="label_view_camera">
+   <property name="geometry">
+    <rect>
+     <x>20</x>
+     <y>30</y>
+     <width>901</width>
+     <height>901</height>
+    </rect>
+   </property>
+   <property name="frameShape">
+    <enum>QFrame::Box</enum>
+   </property>
+   <property name="text">
+    <string>TextLabel</string>
+   </property>
+  </widget>
+  <widget class="QLabel" name="label_info">
+   <property name="geometry">
+    <rect>
+     <x>940</x>
+     <y>330</y>
+     <width>411</width>
+     <height>51</height>
+    </rect>
+   </property>
+   <property name="text">
+    <string>Info:</string>
+   </property>
+  </widget>
+  <widget class="QWidget" name="gridLayoutWidget">
+   <property name="geometry">
+    <rect>
+     <x>930</x>
+     <y>30</y>
+     <width>421</width>
+     <height>291</height>
+    </rect>
+   </property>
+   <layout class="QGridLayout" name="layout_histogram"/>
+  </widget>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

free_swimming_4fish_setup/alignment/camera_alignment_gui.py

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+# -*- coding: utf-8 -*-
+import sys
+import numpy as np
+import os
+from multiprocessing import Process, Value
+import pickle
+import cv2
+from ctypes import *
+import pyqtgraph as pg
+import socket
+
+from PyQt5 import QtGui, QtWidgets, QtCore, Qt, uic
+import sys
+sys._excepthook = sys.excepthook
+def exception_hook(exctype, value, traceback):
+    sys._excepthook(exctype, value, traceback)
+    sys.exit(1)
+sys.excepthook = exception_hook
+
+class Fishreturn(Structure):
+    _fields_ = [("camera_framenum", c_uint),
+                ("camera_timestamp", c_double),
+                ("camera_fps", c_double),
+
+                ("mode_updated", c_bool),
+
+                ("errorcode", c_int),
+
+                ("fish_movie_framenum", c_uint),
+
+                ("fish_position_x", c_double),
+                ("fish_position_y", c_double),
+
+                ("fish_orientation", c_double),
+                ("fish_accumulated_orientation", c_double),
+                ("fish_accumulated_orientation_lowpass", c_double),
+                ("fish_accumulated_orientation_variance", c_double),
+
+                ("fish_accumulated_path", c_double),
+
+                ("bout_found", c_bool),
+                ("bout_timestamp_start", c_double),
+                ("bout_timestamp_end", c_double),
+                ("bout_heading_angle_change", c_double),
+                ("bout_distance_traveled_change", c_double),
+
+                ("fish_area", c_double),
+                ]
+
+
+class keyPressEvent(QtCore.QObject):
+    def __init__(self, parent):
+        super(keyPressEvent, self).__init__(parent)
+        self.parent = parent
+
+
+    def eventFilter(self, object, event):
+        if event.type() == QtCore.QEvent.KeyPress:
+            #print event.key()
+            if event.key() == 16777236:
+                self.parent.xoffset += 2
+
+            if event.key() == 16777234:
+                self.parent.xoffset -= 2
+
+            if event.key() == 16777235:
+                self.parent.yoffset += 2
+
+            if event.key() == 16777237:
+                self.parent.yoffset -= 2
+
+
+            if event.key() == ord('T'):
+                self.parent.radius += 16
+
+            if event.key() == ord('R'):
+                self.parent.radius -= 16 # the width has to be devidable to 32
+
+            if event.key() == ord('G'):
+                self.parent.gain -= 0.05
+
+            if event.key() == ord('H'):
+                self.parent.gain += 0.05
+
+            if event.key() == ord('S'):
+                self.parent.shutter -= 0.05
+
+            if event.key() == ord('D'):
+                self.parent.shutter += 0.05
+
+            if event.key() == 16777216:  # ESC
+                self.parent.close()
+
+        return False # not complete
+
+class CameraAlignment_Dialog(QtWidgets.QDialog):
+    def __init__(self, fish_index, running, parent=None):
+        QtWidgets.QWidget.__init__(self, parent)
+        self.fish_index = fish_index
+        self.running = running
+
+        path = os.path.dirname(__file__)
+        uic.loadUi(os.path.join(path, "camera_alignment.ui"), self)
+
+        computer_name = socket.gethostname()
+
+        if computer_name == "NW152-beh-2":
+            self.setup_ID = 0
+
+        #if computer_name == "NW152-beh-2":
+            #self.setup_ID = 1
+
+
+        if self.setup_ID == 0:
+            self.root_path = r"C:\LS100\LS100_free_swimming_4fish_data"
+            self.lib = cdll.LoadLibrary(r"C:\Users\Max\Desktop\LS100\modules\fishcamera_C\x64\Release\fishcamera.dll")
+
+        #if self.setup_ID == 1:
+            #self.root_path = r"D:\Yasuko_free_swimming_4fish_data"
+            #self.lib = cdll.LoadLibrary(r"C:\Users\Yasuko Isoe\PyCharm_projects\fishsetup\modules\fishcamera_C\x64\Release\fishcamera.dll")
+
+        self.installEventFilter(keyPressEvent(self))
+        self.layout_histogram.installEventFilter(keyPressEvent(self))
+        self.label_view_camera.installEventFilter(keyPressEvent(self))
+
+        self.lib.get_fish_info.restype = Fishreturn
+        self.lib.get_gain.restype = c_double
+        self.lib.get_shutter.restype = c_double
+
+        [self.radius, self.xoffset, self.yoffset, self.gain, self.shutter] = 1024, 0, 0, 0.5, 0.5
+
+
+        if self.setup_ID == 0:
+            if self.fish_index == 0:
+                self.camera_serial = 16307759
+            elif self.fish_index == 1:
+                self.camera_serial = 19300526
+            # elif self.fish_index == 2:
+            #     self.camera_serial = 19242806
+
+        # if self.setup_ID == 1:
+        #
+        #     if self.fish_index == 0:
+        #         self.camera_serial = 16307759
+        #     elif self.fish_index == 1:
+        #         self.camera_serial = 19300526
+            # elif self.fish_index == 2:
+            #     self.camera_serial = 19242806
+
+        try:
+            [self.radius, self.xoffset, self.yoffset, self.gain, self.shutter] = pickle.load(open(os.path.join(self.root_path, "camera_configuration_fish%d.dat"%self.fish_index), 'rb'))
+        except:
+            print("???")
+            pass
+
+        self.lib.open_cam(self.camera_serial, 1024, 0, 0, c_float(self.gain), c_float(self.shutter), c_char_p("".encode()), c_char_p("".encode()), c_char_p("".encode()))
+
+        pg.setConfigOption('background', pg.mkColor(0.95))
+        pg.setConfigOption('foreground', 'k')
+
+        self.my_plot = pg.PlotWidget()
+        self.layout_histogram.addWidget(self.my_plot)
+
+        self.my_plot.setLabel('left', 'Mean Brightness')
+        self.my_plot.setLabel('bottom', 'Normalized radius')
+        self.my_plot.setXRange(0, 1)
+        self.my_plot.setYRange(0, 255)
+
+        curvePen = pg.mkPen(color=(255, 15, 10), width=4.5)
+
+        self.curve = pg.PlotCurveItem(pen = curvePen)
+
+        self.my_plot.addItem(self.curve)
+
+        self.fish_roi_buffer = create_string_buffer(2048*2048)
+
+        self.timer = QtCore.QTimer()
+        self.timer.timeout.connect(self.Refresh)
+        self.timer.start(40.)
+
+    def closeEvent(self, event):
+        print("Closing...")
+
+        self.lib.close_cam()
+        print("Saving configuration file")
+        pickle.dump([self.radius, self.xoffset, self.yoffset, self.gain, self.shutter], open(os.path.join(self.root_path, "camera_configuration_fish%d.dat"%self.fish_index), 'wb'))
+
+        # also tell the panda3d to close
+        self.running.value = 0
+
+        self.close()
+
+    def Refresh(self):
+
+        self.radius = int(self.radius/16)*16
+        self.xoffset = int(self.xoffset/2)*2
+        self.yoffset = int(self.yoffset/2)*2
+
+        self.lib.set_gain(c_double(self.gain))
+        self.lib.set_shutter(c_double(self.shutter))
+
+        rs = np.linspace(0, 500, 100)/500.
+        import datetime
+        t = datetime.datetime.now()
+        self.lib.get_image(self.fish_roi_buffer, 2048*2048)
+
+        roi_ar = np.fromstring(self.fish_roi_buffer, dtype=np.uint8).reshape((2048, 2048))
+        #roi_ar = (np.random.random((2048, 2048))*255).astype(np.uint8)
+        pic = cv2.resize(roi_ar, (500, 500)).flatten()
+
+        radial_histogram = create_string_buffer(100)
+        self.lib.get_radial_histogram(pic.tobytes(), radial_histogram)
+
+        radial_histogram = np.fromstring(radial_histogram, dtype=np.uint8)
+        self.curve.setData(rs, radial_histogram)
+
+        roi_ar = cv2.cvtColor(roi_ar, cv2.COLOR_GRAY2RGBA)
+
+        cv2.circle(roi_ar, (1024+self.xoffset, 1024-self.yoffset), radius = self.radius, color = (0, 255, 255, 255), thickness=3)
+
+        cv2.line(roi_ar, (1024-int(0.5*self.radius)+self.xoffset, 1024-self.yoffset), (1024+int(0.5*self.radius)+self.xoffset, 1024-self.yoffset), color = (0, 255, 255, 255), thickness=3)
+        cv2.line(roi_ar, (1024+self.xoffset, 1024-int(0.5*self.radius)-self.yoffset), (1024+self.xoffset, 1024+int(0.5*self.radius)-self.yoffset), color = (0, 255, 255, 255), thickness=3)
+
+        roi_ar = cv2.resize(roi_ar, (900, 900)) #1800, 1800
+        QI = QtGui.QImage(roi_ar, 900, 900, QtGui.QImage.Format_ARGB32) # 1800, 1800
+
+        self.label_view_camera.setPixmap(QtGui.QPixmap.fromImage(QI))
+
+        text = "Radius: %d; xoffset: %d; yoffset: %d; Gain set : %.2f; Shutter set: %.2f\n"%(self.radius, self.xoffset, self.yoffset, self.gain, self.shutter)
+        text += "Gain actual: %.2f; Shutter actual: %.2f" % (float(self.lib.get_gain()), float(self.lib.get_shutter()))
+        self.label_info.setText(text)
+
+        self.timer.start(40.)
+
+
+class GUI_Process(Process):
+    def __init__(self, fish_index):
+        Process.__init__(self)
+        self.fish_index = fish_index
+
+        self.running = Value("i", 1)
+
+    def run(self):
+        app = QtWidgets.QApplication(sys.argv)
+
+        main = CameraAlignment_Dialog(self.fish_index, self.running)
+
+        main.show()
+        app.exec_()
+

free_swimming_4fish_setup/alignment/clean.py

@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+if __name__ == "__main__":
+    import sys
+
+    from direct.showbase.ShowBase import ShowBase
+    from pandac.PandaModules import *
+
+    class World(ShowBase):
+
+        def __init__(self):
+
+            loadPrcFileData("",
+                    """fullscreen 0
+                       win-origin 1920 0
+                       undecorated 1
+                       win-size 5760 1080
+                       sync-video 0
+                       load-display pandagl""")
+
+            # Init the scene
+            ShowBase.__init__(self)
+            self.disableMouse()
+
+            self.accept("escape", self.finish)
+
+            self.setBackgroundColor(1, 1, 1, 1)
+
+        def finish(self):
+
+            sys.exit()
+
+
+    world = World()
+    world.run()