def setup_camera(self):
self.camera_view = CameraGraphicsView()
self.widget_7.children()[0].addWidget(self.camera_view)
self.camera_scene = QGraphicsScene()
self.camera_view.setScene(self.camera_scene)
self.camera_scene.mousePressEvent = self.camera_pressed
self.camera_scene.mouseMoveEvent = self.camera_moved
self.camera_scene.mouseReleaseEvent = self.camera_released
self.scan_type = 'continuous'
QObject.connect(self.d2, SIGNAL('clicked()'), self.change_selector)
QObject.connect(self.d3, SIGNAL('clicked()'), self.change_selector)
self.d2.click()
self.camera_device = ueye.camera(1)
self.camera_device.AllocImageMem()
self.camera_device.SetImageMem()
self.camera_device.SetImageSize()
self.camera_device.SetColorMode()
self.camera_device.CaptureVideo()
self.camera_timer = QtCore.QTimer()
self.connect(self.camera_timer, QtCore.SIGNAL("timeout()"),
self.update_camera_image_timer)
self.update_camera_image()
self.camera_timer.start(500)
def setup_camera(self):
self.camera_view = CameraGraphicsView()
self.widget_7.children()[0].addWidget(self.camera_view)
self.camera_scene = QGraphicsScene()
self.camera_view.setScene(self.camera_scene)
self.camera_scene.mousePressEvent = self.camera_pressed
self.camera_scene.mouseMoveEvent = self.camera_moved
self.camera_scene.mouseReleaseEvent = self.camera_released
self.scan_type = 'continuous'
QObject.connect(self.d2, SIGNAL('clicked()'), self.change_selector)
QObject.connect(self.d3, SIGNAL('clicked()'), self.change_selector)
self.d2.click()
self.camera_device = ueye.camera(1)
self.camera_device.AllocImageMem()
self.camera_device.SetImageMem()
self.camera_device.SetImageSize()
self.camera_device.SetColorMode()
self.camera_device.CaptureVideo()
self.camera_timer = QtCore.QTimer()
self.connect(self.camera_timer, QtCore.SIGNAL("timeout()"), self.update_camera_image_timer)
self.update_camera_image()
self.camera_timer.start(500)
class OCT(QtGui.QMainWindow, form_class):
def __init__(self, parent=None, selected=[], flag=0, *args):
QtGui.QWidget.__init__(self, parent, *args)
self.setupUi(self)
QObject.connect(self.start, SIGNAL("clicked()"),
self.start_acquisition)
QObject.connect(self.imagej, SIGNAL("clicked()"), self.image_j)
self.config = processor.parse_config()
self.setup_a_scan()
# self.setup_camera()
self.setup_tomography()
self.setup_select_image()
self.processed_data = []
self.current_image = 0
self.setup_show_scale()
self.setup_data_collector()
def setup_data_collector(self):
self.DataCollector = AcquirerProcessor(self)
self.connect(self.DataCollector, SIGNAL("data_ready(PyQt_PyObject)"),
self.add_data_and_update)
self.DataCollector.start()
def setup_show_scale(self):
QObject.connect(self.show_scale_checkbox,
SIGNAL("stateChanged( int )"), self.show_scale_event)
def show_scale_event(self):
if self.show_scale_checkbox.isChecked():
self.make_scale()
else:
self.remove_scale()
def closeEvent(self, event):
pass
# self.camera_timer.stop()
# self.camera_device.StopLiveVideo()
# self.camera_device.FreeImageMem()
# self.camera_device.ExitCamera()
def image_j(self):
filename = self.save_tiff(self.processed_data[self.current_image])
subprocess.Popen(["imagej", '-o', filename], stdout=subprocess.PIPE)
def save_tiff(self, data):
data = data.T
image = Image.frombuffer("L", data.shape, data.data, 'raw', 'L', 0, 1)
fd, filename = tempfile.mkstemp(suffix=".tiff")
with os.fdopen(fd, 'w') as fp:
image.save(fp=fp, format="tiff")
return filename
def setup_select_image(self):
QObject.connect(self.select_image, SIGNAL("valueChanged( int )"),
self.update_image)
def setup_tomography(self):
self.tomography_scene = QGraphicsScene(0, 0, 640, 480)
self.tomography_view.setScene(self.tomography_scene)
self.tomography_scene.mousePressEvent = self.tomography_pressed
self.tomography_scene.mouseMoveEvent = self.tomography_pressed
# self.make_scale()
self.plot_in_tomography_view(np.zeros((480, 640)))
self.tomography_view.fitInView(QRectF(0, 0, 640, 480),
QtCore.Qt.KeepAspectRatio)
# self.tomography_scene.mouseReleaseEvent = self.camera_released
def make_scale(self):
scene_rect = self.tomography_scene.sceneRect()
bl = scene_rect.bottomRight()
size = QtCore.QSizeF(scene_rect.width() / 4, scene_rect.height() / 20)
self.scale_rect = QRectF(
bl - QtCore.QPointF(size.width() + size.height(),
size.height() * 2), size)
self.scale_item = self.tomography_scene.addRect(
self.scale_rect, QPen(Qt.Qt.yellow, 1),
QBrush(Qt.Qt.yellow, Qt.Qt.SolidPattern))
def remove_scale(self):
self.tomography_scene.removeItem(self.scale_item)
def tomography_pressed(self, event):
x = int(event.scenePos().x())
if hasattr(self, "tomography_line_item"):
self.tomography_scene.removeItem(self.tomography_line_item)
yf = int(self.tomography_scene.sceneRect().top())
y0 = int(self.tomography_scene.sceneRect().bottom())
self.tomography_line_item = self.tomography_scene.addLine(
x, y0, x, yf, QPen(Qt.Qt.yellow, 1, Qt.Qt.DotLine))
if x >= self.current_tomography_data.shape[1]:
x = self.current_tomography_data.shape[1] - 1
elif x < 0:
x = 0
Y = self.current_tomography_data[:, x]
X = np.linspace(10, 0, len(Y))
self.curve.setData(Y, X)
self.plot.replot()
def setup_a_scan(self):
self.plot = Qwt.QwtPlot()
size_policy = QSizePolicy()
size_policy.setHorizontalStretch(1)
size_policy.setHorizontalPolicy(size_policy.Preferred)
size_policy.setVerticalPolicy(size_policy.Preferred)
self.plot.setSizePolicy(size_policy)
# self.plot.enableAxis(Qwt.QwtPlot.yLeft, False)
self.plot.enableAxis(Qwt.QwtPlot.xBottom, False)
grid = Qwt.QwtPlotGrid()
grid.attach(self.plot)
grid.setPen(Qt.QPen(Qt.Qt.white, 0, Qt.Qt.DotLine))
self.plot.setCanvasBackground(Qt.Qt.black)
self.plot_holder_widget.children()[0].addWidget(self.plot)
self.curve = Qwt.QwtPlotCurve()
self.curve.attach(self.plot)
self.curve.setPen(Qt.QPen(Qt.Qt.green, 1))
def update_image(self, index):
self.current_image = index - 1
self.plot_in_tomography_view(self.processed_data[self.current_image])
def setup_camera(self):
self.camera_view = CameraGraphicsView()
self.widget_7.children()[0].addWidget(self.camera_view)
self.camera_scene = QGraphicsScene()
self.camera_view.setScene(self.camera_scene)
self.camera_scene.mousePressEvent = self.camera_pressed
self.camera_scene.mouseMoveEvent = self.camera_moved
self.camera_scene.mouseReleaseEvent = self.camera_released
self.scan_type = 'continuous'
QObject.connect(self.d2, SIGNAL('clicked()'), self.change_selector)
QObject.connect(self.d3, SIGNAL('clicked()'), self.change_selector)
self.d2.click()
self.camera_device = ueye.camera(1)
self.camera_device.AllocImageMem()
self.camera_device.SetImageMem()
self.camera_device.SetImageSize()
self.camera_device.SetColorMode()
self.camera_device.CaptureVideo()
self.camera_timer = QtCore.QTimer()
self.connect(self.camera_timer, QtCore.SIGNAL("timeout()"),
self.update_camera_image_timer)
self.update_camera_image()
self.camera_timer.start(500)
def update_camera_image(self):
if hasattr(self, "camera_pixmap"):
self.camera_scene.removeItem(self.camera_pixmap)
self.camera_device.CopyImageMem()
self.camera_image = gray2qimage(self.camera_device.data)
pixmap_image = QtGui.QPixmap.fromImage(self.camera_image)
self.camera_pixmap = self.camera_scene.addPixmap(pixmap_image)
if hasattr(self, 'item'):
self.camera_pixmap.stackBefore(self.item)
self.camera_scene.setSceneRect(self.camera_pixmap.boundingRect())
self.camera_view.fitInView(self.camera_pixmap,
QtCore.Qt.KeepAspectRatio)
def update_camera_image_timer(self):
self.update_camera_image()
self.camera_timer.start(500)
def change_selector(self):
if self.d2.isChecked():
self.scan_type = "continuous"
self.selector = lambda start, end: self.camera_scene.addLine(
QLineF(start, end))
else:
self.scan_type = "3D"
self.selector = self.select_rect
# self.selector = lambda start, end: self.camera_scene.addRect(QRectF(start, end))
def area_select(self, start, end):
return self.camera_scene.addRect(QRectF(start, end))
def camera_pressed(self, event):
self.pressed_pos = event.scenePos()
self.camera_moved(event)
def update_config_path(self, start, end):
start = self.convert_to_path(start)
end = self.convert_to_path(end)
self.config[self.scan_type]['x0'] = start.x()
self.config[self.scan_type]['y0'] = start.y()
self.config[self.scan_type]['xf'] = start.x()
self.config[self.scan_type]['yf'] = start.y()
def convert_to_path(self, point):
scale = self.config['camera_to_path_scale']
return point * scale
def fix_rect_points(self, A, B):
x0 = min([A.x(), B.x()])
xf = max([A.x(), B.x()])
y0 = min([A.y(), B.y()])
yf = max([A.y(), B.y()])
return QPointF(x0, y0), QPointF(xf, yf)
def camera_moved(self, event):
if hasattr(self, "item"):
self.camera_scene.removeItem(self.item)
# start, end = self.fix_rect_points(self.pressed_pos, event.scenePos())
start, end = self.pressed_pos, event.scenePos()
self.item = self.selector(start, end)
def camera_released(self, event):
if hasattr(self, "item"):
self.camera_scene.removeItem(self.item)
self.released_pos = event.scenePos()
# start, end = self.fix_rect_points(self.pressed_pos, event.scenePos())
start, end = self.pressed_pos, event.scenePos()
self.update_config_path(start, end)
self.item = self.selector(start, end)
def select_rect(self, start, end):
start, end = self.fix_rect_points(start, end)
return self.camera_scene.addRect(QRectF(start, end))
def save_processed_data(self, filename):
import h5py
file = h5py.File(filename, 'w')
root = file.create_group("root")
for i, image in enumerate(self.processed_data):
root.create_dataset('image_%03d' % i, image.shape, image.dtype)
file.close()
def plot_in_tomography_view(self, data):
self.current_tomography_data = data
if hasattr(self, "tomography_item"):
self.tomography_scene.removeItem(self.tomography_item)
self.tomography_image = gray2qimage(data)
# self.resize_tomography_view()
self.tomography_scene.setBackgroundBrush(
QtGui.QBrush(self.tomography_image))
# self.resize_tomography_view()
self.tomography_view.fitInView(self.tomography_scene.sceneRect(),
QtCore.Qt.KeepAspectRatio)
def resize_tomography_view(self):
holder_aspect_ratio = aspect_ratio(
self.tomography_holder_widget.rect())
tomography_aspect_ratio = aspect_ratio(self.tomography_image)
if holder_aspect_ratio > tomography_aspect_ratio:
width = self.tomography_holder_widget.width()
self.tomography_view.setFixedHeight(tomography_aspect_ratio *
width)
self.tomography_view.setFixedWidth(width)
else:
height = self.tomography_holder_widget.height()
self.tomography_view.setFixedWidth(height /
tomography_aspect_ratio)
self.tomography_view.setFixedHeight(height)
def add_data_and_update(self, data):
logger.debug("std dev %.2e" % np.std(data))
self.plot_in_tomography_view(data)
self.processed_data += [data]
n_images = len(self.processed_data)
self.current_image = n_images - 1
self.select_image.setMaximum(n_images)
def start_acquisition(self):
cmd = [
"python", "doct.py", "-o", self.config['raw_file'], "--scan-single"
]
self.acquisition = subprocess.Popen(cmd)
def save_serie(self):
if save_serie_dialog._exec():
print save_serie_dialog.save_file_path.text()
class OCT (QtGui.QMainWindow, form_class):
def __init__(self,parent = None, selected = [], flag = 0, *args):
QtGui.QWidget.__init__(self, parent, *args)
self.setupUi(self)
QObject.connect(self.start, SIGNAL("clicked()"), self.start_acquisition)
QObject.connect(self.imagej, SIGNAL("clicked()"), self.image_j)
self.config = processor.parse_config()
self.setup_a_scan()
# self.setup_camera()
self.setup_tomography()
self.setup_select_image()
self.processed_data = []
self.current_image = 0
self.setup_show_scale()
self.setup_data_collector()
def setup_data_collector(self):
self.DataCollector = AcquirerProcessor(self)
self.connect(self.DataCollector, SIGNAL("data_ready(PyQt_PyObject)"), self.add_data_and_update)
self.DataCollector.start()
def setup_show_scale(self):
QObject.connect(self.show_scale_checkbox, SIGNAL("stateChanged( int )"), self.show_scale_event)
def show_scale_event(self):
if self.show_scale_checkbox.isChecked():
self.make_scale()
else :
self.remove_scale()
def closeEvent(self, event):
pass
# self.camera_timer.stop()
# self.camera_device.StopLiveVideo()
# self.camera_device.FreeImageMem()
# self.camera_device.ExitCamera()
def image_j(self):
filename = self.save_tiff(self.processed_data[self.current_image])
subprocess.Popen(["imagej", '-o', filename], stdout = subprocess.PIPE)
def save_tiff(self, data):
data = data.T
image = Image.frombuffer("L" ,data.shape ,data.data, 'raw', 'L', 0 ,1)
fd, filename = tempfile.mkstemp(suffix = ".tiff")
with os.fdopen(fd, 'w') as fp:
image.save(fp = fp, format = "tiff")
return filename
def setup_select_image(self):
QObject.connect(self.select_image, SIGNAL("valueChanged( int )"), self.update_image)
def setup_tomography(self):
self.tomography_scene = QGraphicsScene(0,0,640,480)
self.tomography_view.setScene(self.tomography_scene)
self.tomography_scene.mousePressEvent = self.tomography_pressed
self.tomography_scene.mouseMoveEvent = self.tomography_pressed
# self.make_scale()
self.plot_in_tomography_view(np.zeros((480,640)))
self.tomography_view.fitInView(QRectF(0,0,640,480), QtCore.Qt.KeepAspectRatio)
# self.tomography_scene.mouseReleaseEvent = self.camera_released
def make_scale(self):
scene_rect = self.tomography_scene.sceneRect()
bl = scene_rect.bottomRight()
size = QtCore.QSizeF(scene_rect.width()/4,scene_rect.height()/20)
self.scale_rect = QRectF(bl - QtCore.QPointF(size.width()+size.height(),size.height()*2), size)
self.scale_item = self.tomography_scene.addRect(self.scale_rect, QPen(Qt.Qt.yellow, 1), QBrush(Qt.Qt.yellow, Qt.Qt.SolidPattern))
def remove_scale(self):
self.tomography_scene.removeItem(self.scale_item)
def tomography_pressed(self, event):
x = int(event.scenePos().x())
if hasattr(self, "tomography_line_item"):
self.tomography_scene.removeItem(self.tomography_line_item)
yf = int(self.tomography_scene.sceneRect().top())
y0 = int(self.tomography_scene.sceneRect().bottom())
self.tomography_line_item = self.tomography_scene.addLine(x, y0, x, yf, QPen(Qt.Qt.yellow, 1, Qt.Qt.DotLine))
if x >= self.current_tomography_data.shape[1]:
x = self.current_tomography_data.shape[1] - 1
elif x < 0:
x = 0
Y = self.current_tomography_data[:,x]
X = np.linspace(10,0,len(Y))
self.curve.setData(Y,X)
self.plot.replot()
def setup_a_scan(self):
self.plot = Qwt.QwtPlot()
size_policy = QSizePolicy()
size_policy.setHorizontalStretch(1)
size_policy.setHorizontalPolicy(size_policy.Preferred)
size_policy.setVerticalPolicy(size_policy.Preferred)
self.plot.setSizePolicy(size_policy)
# self.plot.enableAxis(Qwt.QwtPlot.yLeft, False)
self.plot.enableAxis(Qwt.QwtPlot.xBottom, False)
grid = Qwt.QwtPlotGrid()
grid.attach(self.plot)
grid.setPen(Qt.QPen(Qt.Qt.white, 0, Qt.Qt.DotLine))
self.plot.setCanvasBackground(Qt.Qt.black)
self.plot_holder_widget.children()[0].addWidget(self.plot)
self.curve = Qwt.QwtPlotCurve()
self.curve.attach(self.plot)
self.curve.setPen(Qt.QPen(Qt.Qt.green, 1))
def update_image(self, index):
self.current_image = index - 1
self.plot_in_tomography_view(self.processed_data[self.current_image])
def setup_camera(self):
self.camera_view = CameraGraphicsView()
self.widget_7.children()[0].addWidget(self.camera_view)
self.camera_scene = QGraphicsScene()
self.camera_view.setScene(self.camera_scene)
self.camera_scene.mousePressEvent = self.camera_pressed
self.camera_scene.mouseMoveEvent = self.camera_moved
self.camera_scene.mouseReleaseEvent = self.camera_released
self.scan_type = 'continuous'
QObject.connect(self.d2, SIGNAL('clicked()'), self.change_selector)
QObject.connect(self.d3, SIGNAL('clicked()'), self.change_selector)
self.d2.click()
self.camera_device = ueye.camera(1)
self.camera_device.AllocImageMem()
self.camera_device.SetImageMem()
self.camera_device.SetImageSize()
self.camera_device.SetColorMode()
self.camera_device.CaptureVideo()
self.camera_timer = QtCore.QTimer()
self.connect(self.camera_timer, QtCore.SIGNAL("timeout()"), self.update_camera_image_timer)
self.update_camera_image()
self.camera_timer.start(500)
def update_camera_image(self):
if hasattr(self,"camera_pixmap"):
self.camera_scene.removeItem(self.camera_pixmap)
self.camera_device.CopyImageMem()
self.camera_image = gray2qimage(self.camera_device.data)
pixmap_image = QtGui.QPixmap.fromImage(self.camera_image)
self.camera_pixmap = self.camera_scene.addPixmap(pixmap_image)
if hasattr(self, 'item'):
self.camera_pixmap.stackBefore(self.item)
self.camera_scene.setSceneRect(self.camera_pixmap.boundingRect())
self.camera_view.fitInView(self.camera_pixmap, QtCore.Qt.KeepAspectRatio)
def update_camera_image_timer(self):
self.update_camera_image()
self.camera_timer.start(500)
def change_selector(self):
if self.d2.isChecked():
self.scan_type = "continuous"
self.selector = lambda start, end: self.camera_scene.addLine(QLineF(start, end))
else:
self.scan_type = "3D"
self.selector = self.select_rect
# self.selector = lambda start, end: self.camera_scene.addRect(QRectF(start, end))
def area_select(self, start, end):
return self.camera_scene.addRect(QRectF(start, end))
def camera_pressed(self, event):
self.pressed_pos = event.scenePos()
self.camera_moved(event)
def update_config_path(self, start, end):
start = self.convert_to_path(start)
end = self.convert_to_path(end)
self.config[self.scan_type]['x0'] = start.x()
self.config[self.scan_type]['y0'] = start.y()
self.config[self.scan_type]['xf'] = start.x()
self.config[self.scan_type]['yf'] = start.y()
def convert_to_path(self, point):
scale = self.config['camera_to_path_scale']
return point*scale
def fix_rect_points(self, A, B):
x0 = min([A.x(), B.x()])
xf = max([A.x(), B.x()])
y0 = min([A.y(), B.y()])
yf = max([A.y(), B.y()])
return QPointF(x0, y0), QPointF(xf, yf)
def camera_moved(self, event):
if hasattr(self, "item"):
self.camera_scene.removeItem(self.item)
# start, end = self.fix_rect_points(self.pressed_pos, event.scenePos())
start, end = self.pressed_pos, event.scenePos()
self.item = self.selector(start, end)
def camera_released(self, event):
if hasattr(self, "item"):
self.camera_scene.removeItem(self.item)
self.released_pos = event.scenePos()
# start, end = self.fix_rect_points(self.pressed_pos, event.scenePos())
start, end = self.pressed_pos, event.scenePos()
self.update_config_path(start, end)
self.item = self.selector(start, end)
def select_rect(self, start, end):
start, end = self.fix_rect_points(start, end)
return self.camera_scene.addRect(QRectF(start, end))
def save_processed_data(self, filename):
import h5py
file = h5py.File(filename, 'w')
root = file.create_group("root")
for i, image in enumerate(self.processed_data):
root.create_dataset('image_%03d'%i, image.shape, image.dtype)
file.close()
def plot_in_tomography_view(self, data):
self.current_tomography_data = data
if hasattr(self, "tomography_item"):
self.tomography_scene.removeItem(self.tomography_item)
self.tomography_image = gray2qimage(data)
# self.resize_tomography_view()
self.tomography_scene.setBackgroundBrush(QtGui.QBrush(self.tomography_image))
# self.resize_tomography_view()
self.tomography_view.fitInView(self.tomography_scene.sceneRect(), QtCore.Qt.KeepAspectRatio)
def resize_tomography_view(self):
holder_aspect_ratio = aspect_ratio(self.tomography_holder_widget.rect())
tomography_aspect_ratio = aspect_ratio(self.tomography_image)
if holder_aspect_ratio > tomography_aspect_ratio:
width = self.tomography_holder_widget.width()
self.tomography_view.setFixedHeight(tomography_aspect_ratio*width)
self.tomography_view.setFixedWidth(width)
else:
height = self.tomography_holder_widget.height()
self.tomography_view.setFixedWidth(height/tomography_aspect_ratio)
self.tomography_view.setFixedHeight(height)
def add_data_and_update(self, data):
logger.debug("std dev %.2e"%np.std(data))
self.plot_in_tomography_view(data)
self.processed_data += [data]
n_images = len(self.processed_data)
self.current_image = n_images - 1
self.select_image.setMaximum(n_images)
def start_acquisition(self):
cmd = ["python", "doct.py", "-o", self.config['raw_file'], "--scan-single" ]
self.acquisition = subprocess.Popen(cmd)
def save_serie(self):
if save_serie_dialog._exec():
print save_serie_dialog.save_file_path.text()
