def __init__(self):
QtGui.QWidget.__init__(self)
self._im_view = PixmapStackView()
self._label = ScalableLabel()
self._layout = QtGui.QVBoxLayout(self)
self._layout.addWidget(self._label)
self._label.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
self.connect(self._label, QtCore.SIGNAL("mouse_press"), self.mouse_pressed)
self.connect(self._label, QtCore.SIGNAL("mouse_move"), self.mouse_pressed)
self.axis = 2
self.inc = 1 # index increment
self._palette_name = None
def __init__ (self) :
QMainWindow.__init__(self)
# points
self._points = []
self._id_gen = IdSetGenerator()
#X self.version = 2
self._view = PixmapStackView()
#QGraphicsScene
self._scene = QGraphicsScene()
#QGraphicsPixmapItem
self._item = QGraphicsPixmapItem()
self._item.setTransformationMode(Qt.SmoothTransformation)
self._item.setFlag(self._item.ItemIsSelectable,False)
self._scene.addItem(self._item)
#QGraphicsView
self._widget = ScalableGraphicsView(self._scene)
self.setCentralWidget(self._widget)
################### mouse handling ###################
self._widget.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
self._last_slice = 0
QObject.connect(self._widget,
SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._widget,
SIGNAL("mouse_move"),
self.mouse_moved)
QObject.connect(self,
SIGNAL("mouse_moved"),
self.coordinates)
################### menubar ###################
self.menu = self.menuBar()
self.menu_file = self.menu.addMenu('File')
# Import Points
self._load_points = self.menu_file.addAction('Import Points')
QObject.connect(self._load_points,
SIGNAL("triggered(bool)"),
self.load_points)
# Save points
self._save_points = self.menu_file.addAction('Save Points')
QObject.connect(self._save_points,
SIGNAL("triggered(bool)"),
self.save_points)
################### toolbar ###################
self._toolbar = self.addToolBar("tools")
self._toolgroup = QActionGroup(self)
# QWidgetAction : "Rotation Left"
self._action_left = self._toolbar.addAction("left rotation")
self._action_left.setIcon(QIcon(":/image/rotate_left.png") )
QObject.connect(self._action_left,
SIGNAL("triggered(bool)"),
self.rotate_left)
# QWidgetAction : "Rotation Right"
self._action_right = self._toolbar.addAction("right rotation")
self._action_right.setIcon(QIcon(":/image/rotate_right.png") )
QObject.connect(self._action_right,
SIGNAL("triggered(bool)"),
self.rotate_right)
# QWidgetAction : "Add point"
self._action_add = self._toolbar.addAction("Add point")
self._action_add.setCheckable(True)
self._toolgroup.addAction(self._action_add)
self._action_add.setIcon(QIcon(":/image/add.png") )
# QWidgetAction : "Delete point"
self._action_delete = self._toolbar.addAction("Delete point")
self._action_delete.setCheckable(True)
self._toolgroup.addAction(self._action_delete)
self._action_delete.setIcon(QIcon(":/image/delete.png") )
################### palette ###################
self._palette_select = QComboBox()
self._toolbar.addWidget(self._palette_select)
for palname in palette_names :
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
################### slider ###################
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setRange(0,self._view.nb_slices() - 1)
QObject.connect(self._img_slider,
SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea,self._bot_toolbar)
################### statusbar ###################
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.statusbar = self.statusBar()
self.statusbar.addPermanentWidget(self._lab_coord)
self.statusbar.addPermanentWidget(self._lab_xcoord)
self.statusbar.addPermanentWidget(self._lab_ycoord)
self.statusbar.addPermanentWidget(self._lab_zcoord)
self.statusbar.addPermanentWidget(self._lab_intens)
class ImageStackViewerWidget(QtGui.QWidget):
"""
Widget based on openalea.image.gui.slide_viewer.PixmapStackView
"""
valueChanged = QtCore.Signal(object)
stackChanged = QtCore.Signal(object)
def __init__(self):
QtGui.QWidget.__init__(self)
self._im_view = PixmapStackView()
self._label = ScalableLabel()
self._layout = QtGui.QVBoxLayout(self)
self._layout.addWidget(self._label)
self._label.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
self.connect(self._label, QtCore.SIGNAL("mouse_press"), self.mouse_pressed)
self.connect(self._label, QtCore.SIGNAL("mouse_move"), self.mouse_pressed)
self.axis = 2
self.inc = 1 # index increment
self._palette_name = None
##############################################
# Qt Control API
##############################################
def setValue(self, img):
if img is self.value():
return
self._im_view.set_image(img)
try:
self.resolution = img.resolution[:]
except AttributeError:
pass
self._im_view._reconstruct_pixmaps()
self.change_axis(0)
self.slice_changed((0 + self._im_view.nb_slices() - 1) / 2)
self.emit_stack_changed()
def value(self):
return self._im_view.image()
##############################################
# slots
##############################################
def emit_stack_changed(self):
img = self.value()
if img is None:
self.stackChanged.emit(None)
else:
args = dict(shape=img.shape, axis=self.axis,
slice=self._im_view.current_slice(),
resolution=self.resolution, inc=self.inc,
palette_name=self._palette_name)
self.stackChanged.emit(args)
def change_axis(self, ind):
if self.axis == ind:
return
try:
res = list(self.resolution)
del res[self.axis]
tr = self._im_view._transform
print res
if tr % 180:
self._label._resolution = res[1], res[0]
else:
self._label.set_resolution(*res[:2])
except AttributeError:
pass
self._im_view._reconstruct_pixmaps(self.axis)
self.emit_stack_changed()
self.update_pix()
#self.fill_infos()
def mouse_pressed(self, event):
self._last_mouse_x = event.x()
self._last_mouse_y = event.y()
def change_palette(self, palette_name):
if palette_name == self._palette_name:
return
self._palette_name = palette_name
self.emit_stack_changed()
img = self._im_view.image()
if img is None:
return
palette = palette_factory(palette_name, img.max())
self._im_view.set_palette(palette, self.axis)
self.update_pix()
def update_pix(self):
pix = self._im_view.pixmap()
if pix is not None:
self._label.setPixmap(pix)
def get_pixel_value_str(self, img, x, y, z):
px = img[x, y, z]
if isinstance(px, np.ndarray):
return str(px)
else:
return "%3d" % px
def slice_changed(self, ind):
img = self.value()
if img is None:
return
if ind >= img.shape[self.axis]:
ind = img.shape[self.axis] - 1
if ind < 0:
ind = 0
if self._im_view.current_slice() == ind:
return
self._im_view.set_current_slice(ind)
self.emit_stack_changed()
self.update_pix()
def snapshot(self):
"""write the current image
"""
pix = self._im_view.pixmap()
if pix is not None:
pix.save("slice%.4d.png" % self.panel.img_slider.value())
def wheelEvent(self, event):
self.inc = event.delta() / 8 / 15
idx = self._im_view.current_slice()
self.slice_changed(idx + self.inc)
def rotate_left(self):
res = self._label._resolution
self._label._resolution = res[1], res[0]
self._im_view.rotate(-1)
self.update_pix()
def rotate_right(self):
res = self._label._resolution
self._label._resolution = res[1], res[0]
self._im_view.rotate(1)
self.update_pix()
def __init__ (self, parent=None) :
QMainWindow.__init__(self, parent)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.axis = 2
#central label
self._im_view = PixmapStackView()
self._label = ScalableLabel()
self.setCentralWidget(self._label)
#mouse handling
self._label.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
QObject.connect(self._label,
SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._label,
SIGNAL("mouse_move"),
self.mouse_pressed)
#toolbar
QObject.connect(self.ui.action_close,
SIGNAL("triggered(bool)"),
self.close)
QObject.connect(self.ui.action_snapshot,
SIGNAL("triggered(bool)"),
self.snapshot)
QObject.connect(self.ui.action_rotate_left,
SIGNAL("triggered(bool)"),
self.rotate_left)
QObject.connect(self.ui.action_rotate_right,
SIGNAL("triggered(bool)"),
self.rotate_right)
#palette
self._palette_select = QComboBox()
self.ui.toolbar.addWidget(self._palette_select)
for palname in palette_names :
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
#axis
self._axis = QComboBox(self)
self.ui.toolbar.addWidget(self._axis)
self._axis.addItem("Z-axis")
self._axis.addItem("Y-axis")
self._axis.addItem("X-axis")
self.connect(self._axis, SIGNAL('currentIndexChanged(int)'), self.change_axis )
#slider
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setEnabled(False)
QObject.connect(self._img_slider,
SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea,self._bot_toolbar)
#statusbar
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.ui.statusbar.addPermanentWidget(self._lab_coord)
self.ui.statusbar.addPermanentWidget(self._lab_xcoord)
self.ui.statusbar.addPermanentWidget(self._lab_ycoord)
self.ui.statusbar.addPermanentWidget(self._lab_zcoord)
self.ui.statusbar.addPermanentWidget(self._lab_intens)
self.set_title("<"+str(self.viewer_count)+">")
SlideViewer.viewer_count += 1
class PointSelection (QMainWindow) :
def __init__ (self) :
QMainWindow.__init__(self)
# points
self._points = []
self._id_gen = IdSetGenerator()
#X self.version = 2
self._view = PixmapStackView()
#QGraphicsScene
self._scene = QGraphicsScene()
#QGraphicsPixmapItem
self._item = QGraphicsPixmapItem()
self._item.setTransformationMode(Qt.SmoothTransformation)
self._item.setFlag(self._item.ItemIsSelectable,False)
self._scene.addItem(self._item)
#QGraphicsView
self._widget = ScalableGraphicsView(self._scene)
self.setCentralWidget(self._widget)
################### mouse handling ###################
self._widget.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
self._last_slice = 0
QObject.connect(self._widget,
SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._widget,
SIGNAL("mouse_move"),
self.mouse_moved)
QObject.connect(self,
SIGNAL("mouse_moved"),
self.coordinates)
################### menubar ###################
self.menu = self.menuBar()
self.menu_file = self.menu.addMenu('File')
# Import Points
self._load_points = self.menu_file.addAction('Import Points')
QObject.connect(self._load_points,
SIGNAL("triggered(bool)"),
self.load_points)
# Save points
self._save_points = self.menu_file.addAction('Save Points')
QObject.connect(self._save_points,
SIGNAL("triggered(bool)"),
self.save_points)
################### toolbar ###################
self._toolbar = self.addToolBar("tools")
self._toolgroup = QActionGroup(self)
# QWidgetAction : "Rotation Left"
self._action_left = self._toolbar.addAction("left rotation")
self._action_left.setIcon(QIcon(":/image/rotate_left.png") )
QObject.connect(self._action_left,
SIGNAL("triggered(bool)"),
self.rotate_left)
# QWidgetAction : "Rotation Right"
self._action_right = self._toolbar.addAction("right rotation")
self._action_right.setIcon(QIcon(":/image/rotate_right.png") )
QObject.connect(self._action_right,
SIGNAL("triggered(bool)"),
self.rotate_right)
# QWidgetAction : "Add point"
self._action_add = self._toolbar.addAction("Add point")
self._action_add.setCheckable(True)
self._toolgroup.addAction(self._action_add)
self._action_add.setIcon(QIcon(":/image/add.png") )
# QWidgetAction : "Delete point"
self._action_delete = self._toolbar.addAction("Delete point")
self._action_delete.setCheckable(True)
self._toolgroup.addAction(self._action_delete)
self._action_delete.setIcon(QIcon(":/image/delete.png") )
################### palette ###################
self._palette_select = QComboBox()
self._toolbar.addWidget(self._palette_select)
for palname in palette_names :
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
################### slider ###################
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setRange(0,self._view.nb_slices() - 1)
QObject.connect(self._img_slider,
SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea,self._bot_toolbar)
################### statusbar ###################
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.statusbar = self.statusBar()
self.statusbar.addPermanentWidget(self._lab_coord)
self.statusbar.addPermanentWidget(self._lab_xcoord)
self.statusbar.addPermanentWidget(self._lab_ycoord)
self.statusbar.addPermanentWidget(self._lab_zcoord)
self.statusbar.addPermanentWidget(self._lab_intens)
##############################################
#
# update GUI
#
##############################################
def update_pix (self) :
"""
"""
pix = self._view.pixmap()
if pix is not None :
self._item.setPixmap(pix)
else:
print 'None pixmap'
#update points
ind = self._view.current_slice()
for point in self._points :
if point is not None:
pid,item, x,y,z,textid = point
visible = abs(z - ind) < 5
item.setVisible(visible)
col = QColor.fromHsv( (pid * 10) % 360,255,255)
if visible :
sca = max(0.,(5 - abs(z - ind) ) / 5.)
if z == ind :
pen = QPen(QColor(255,255,255) )
pen.setWidthF(2.)
item.setPen(pen)
textid.setVisible(True)
else :
pen = QPen(QColor(0,0,0) )
pen.setWidthF(2.)
item.setPen(pen)
textid.setVisible(False)
else :
sca = 1.
tr = QTransform()
tr.scale(sca,sca)
item.setTransform(tr)
item.update()
def coordinates (self,(i,j,k)) :
self._last_mouse_x,self._last_mouse_y, self._last_slice = i,j,k
self.fill_infos()
class SlideViewer (QMainWindow) :
"""Display each image in a stack using a slider
"""
viewer_count = 0
def __init__ (self, parent=None) :
QMainWindow.__init__(self, parent)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.axis = 2
#central label
self._im_view = PixmapStackView()
self._label = ScalableLabel()
self.setCentralWidget(self._label)
#mouse handling
self._label.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
QObject.connect(self._label,
SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._label,
SIGNAL("mouse_move"),
self.mouse_pressed)
#toolbar
QObject.connect(self.ui.action_close,
SIGNAL("triggered(bool)"),
self.close)
QObject.connect(self.ui.action_snapshot,
SIGNAL("triggered(bool)"),
self.snapshot)
QObject.connect(self.ui.action_rotate_left,
SIGNAL("triggered(bool)"),
self.rotate_left)
QObject.connect(self.ui.action_rotate_right,
SIGNAL("triggered(bool)"),
self.rotate_right)
#palette
self._palette_select = QComboBox()
self.ui.toolbar.addWidget(self._palette_select)
for palname in palette_names :
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
#axis
self._axis = QComboBox(self)
self.ui.toolbar.addWidget(self._axis)
self._axis.addItem("Z-axis")
self._axis.addItem("Y-axis")
self._axis.addItem("X-axis")
self.connect(self._axis, SIGNAL('currentIndexChanged(int)'), self.change_axis )
#slider
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setEnabled(False)
QObject.connect(self._img_slider,
SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea,self._bot_toolbar)
#statusbar
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.ui.statusbar.addPermanentWidget(self._lab_coord)
self.ui.statusbar.addPermanentWidget(self._lab_xcoord)
self.ui.statusbar.addPermanentWidget(self._lab_ycoord)
self.ui.statusbar.addPermanentWidget(self._lab_zcoord)
self.ui.statusbar.addPermanentWidget(self._lab_intens)
self.set_title("<"+str(self.viewer_count)+">")
SlideViewer.viewer_count += 1
##############################################
#
# update GUI
#
##############################################
def update_pix (self) :
pix = self._im_view.pixmap()
if pix is not None :
self._label.setPixmap(pix)
def get_pixel_value_str(self, img, x, y, z):
px = img[x,y,z]
if isinstance(px, np.ndarray):
return str(px)
else:
return "%3d"%px
def fill_infos (self) :
x,y = self._label.pixmap_coordinates(self._last_mouse_x,
self._last_mouse_y)
img = self._im_view.image()
if img is not None :
i,j,k = self._im_view.data_coordinates(x,y)
self._lab_xcoord.setText("% 4d" % i)
self._lab_ycoord.setText("% 4d" % j)
self._lab_zcoord.setText("% 4d" % k)
imax,jmax,kmax = img.shape[:3]
if self.axis==0 : #axis x
if 0 <= i < jmax and 0 <= j < kmax and 0 <= k < imax :
self._lab_intens.setText("intens: %s" % self.get_pixel_value_str(img,k,i,j))
else :
self._lab_intens.setText("intens: None")
elif self.axis==1 : #axis y
if 0 <= i < imax and 0 <= j < kmax and 0 <= k < jmax :
self._lab_intens.setText("intens: %s" % self.get_pixel_value_str(img,i,k,j))
else :
self._lab_intens.setText("intens: None")
else : #axis z
if 0 <= i < imax and 0 <= j < jmax and 0 <= k < kmax :
self._lab_intens.setText("intens: %s" % self.get_pixel_value_str(img,i,j,k))
else :
self._lab_intens.setText("intens: None")
##############################################
#
# accessors
#
##############################################
def set_image (self, img) :
self._im_view.set_image(img)
try :
self.resolution = img.resolution[:]
except AttributeError :
pass
self._img_slider.setRange(0,self._im_view.nb_slices() - 1)
self._img_slider.setEnabled(True)
self.slice_changed(self._img_slider.value() )
def set_palette (self, palette, palette_name = None) :
if palette_name is not None :
ind = self._palette_select.findText(palette_name)
self._palette_select.setCurrentIndex(ind)
self._im_view.set_palette(palette,self.axis)
self.update_pix()
def set_title(self, title=None):
if title is not None :
self.setWindowTitle(title)
def change_axis(self,ind):
self.axis = 2-ind
try :
res = list(self.resolution)
del res[self.axis]
tr = self._im_view._transform
if tr % 180 :
self._label._resolution=res[1],res[0]
else :
self._label.set_resolution(*res)
except AttributeError :
pass
self._im_view._reconstruct_pixmaps(self.axis)
self._img_slider.setRange(0,self._im_view.nb_slices() - 1)
self._img_slider.setEnabled(True)
self.update_pix()
#self.fill_infos()
##############################################
#
# slots
#
##############################################
def palette_name_changed (self, palette_index) :
palname = str(self._palette_select.currentText() )
img = self._im_view.image()
if img is not None :
self.set_palette(palette_factory(str(palname),img.max()) )
def slice_changed (self, ind) :
self._im_view.set_current_slice(ind)
self.update_pix()
self.fill_infos()
def snapshot (self) :
"""write the current image
"""
pix = self._im_view.pixmap()
if pix is not None :
pix.save("slice%.4d.png" % self._img_slider.value() )
def wheelEvent (self, event) :
inc = event.delta() / 8 / 15
self._img_slider.setValue(self._img_slider.value() + inc)
def rotate_left (self) :
res=self._label._resolution
self._label._resolution=res[1],res[0]
self._im_view.rotate(-1)
self.update_pix()
def rotate_right (self) :
res=self._label._resolution
self._label._resolution=res[1],res[0]
self._im_view.rotate(1)
self.update_pix()
def mouse_pressed (self, event) :
self._last_mouse_x = event.x()
self._last_mouse_y = event.y()
self.fill_infos()
def __init__(self):
QMainWindow.__init__(self)
# points
self._points = []
self._id_gen = IdSetGenerator()
#X self.version = 2
self._view = PixmapStackView()
#QGraphicsScene
self._scene = QGraphicsScene()
#QGraphicsPixmapItem
self._item = QGraphicsPixmapItem()
self._item.setTransformationMode(Qt.SmoothTransformation)
self._item.setFlag(self._item.ItemIsSelectable, False)
self._scene.addItem(self._item)
#QGraphicsView
self._widget = ScalableGraphicsView(self._scene)
self.setCentralWidget(self._widget)
################### mouse handling ###################
self._widget.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
self._last_slice = 0
QObject.connect(self._widget, SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._widget, SIGNAL("mouse_move"), self.mouse_moved)
QObject.connect(self, SIGNAL("mouse_moved"), self.coordinates)
################### menubar ###################
self.menu = self.menuBar()
self.menu_file = self.menu.addMenu('File')
# Import Points
self._load_points = self.menu_file.addAction('Import Points')
QObject.connect(self._load_points, SIGNAL("triggered(bool)"),
self.load_points)
# Save points
self._save_points = self.menu_file.addAction('Save Points')
QObject.connect(self._save_points, SIGNAL("triggered(bool)"),
self.save_points)
################### toolbar ###################
self._toolbar = self.addToolBar("tools")
self._toolgroup = QActionGroup(self)
# QWidgetAction : "Rotation Left"
self._action_left = self._toolbar.addAction("left rotation")
self._action_left.setIcon(QIcon(":/image/rotate_left.png"))
QObject.connect(self._action_left, SIGNAL("triggered(bool)"),
self.rotate_left)
# QWidgetAction : "Rotation Right"
self._action_right = self._toolbar.addAction("right rotation")
self._action_right.setIcon(QIcon(":/image/rotate_right.png"))
QObject.connect(self._action_right, SIGNAL("triggered(bool)"),
self.rotate_right)
# QWidgetAction : "Add point"
self._action_add = self._toolbar.addAction("Add point")
self._action_add.setCheckable(True)
self._toolgroup.addAction(self._action_add)
self._action_add.setIcon(QIcon(":/image/add.png"))
# QWidgetAction : "Delete point"
self._action_delete = self._toolbar.addAction("Delete point")
self._action_delete.setCheckable(True)
self._toolgroup.addAction(self._action_delete)
self._action_delete.setIcon(QIcon(":/image/delete.png"))
################### palette ###################
self._palette_select = QComboBox()
self._toolbar.addWidget(self._palette_select)
for palname in palette_names:
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
################### slider ###################
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setRange(0, self._view.nb_slices() - 1)
QObject.connect(self._img_slider, SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea, self._bot_toolbar)
################### statusbar ###################
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.statusbar = self.statusBar()
self.statusbar.addPermanentWidget(self._lab_coord)
self.statusbar.addPermanentWidget(self._lab_xcoord)
self.statusbar.addPermanentWidget(self._lab_ycoord)
self.statusbar.addPermanentWidget(self._lab_zcoord)
self.statusbar.addPermanentWidget(self._lab_intens)
class PointSelection(QMainWindow):
def __init__(self):
QMainWindow.__init__(self)
# points
self._points = []
self._id_gen = IdSetGenerator()
#X self.version = 2
self._view = PixmapStackView()
#QGraphicsScene
self._scene = QGraphicsScene()
#QGraphicsPixmapItem
self._item = QGraphicsPixmapItem()
self._item.setTransformationMode(Qt.SmoothTransformation)
self._item.setFlag(self._item.ItemIsSelectable, False)
self._scene.addItem(self._item)
#QGraphicsView
self._widget = ScalableGraphicsView(self._scene)
self.setCentralWidget(self._widget)
################### mouse handling ###################
self._widget.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
self._last_slice = 0
QObject.connect(self._widget, SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._widget, SIGNAL("mouse_move"), self.mouse_moved)
QObject.connect(self, SIGNAL("mouse_moved"), self.coordinates)
################### menubar ###################
self.menu = self.menuBar()
self.menu_file = self.menu.addMenu('File')
# Import Points
self._load_points = self.menu_file.addAction('Import Points')
QObject.connect(self._load_points, SIGNAL("triggered(bool)"),
self.load_points)
# Save points
self._save_points = self.menu_file.addAction('Save Points')
QObject.connect(self._save_points, SIGNAL("triggered(bool)"),
self.save_points)
################### toolbar ###################
self._toolbar = self.addToolBar("tools")
self._toolgroup = QActionGroup(self)
# QWidgetAction : "Rotation Left"
self._action_left = self._toolbar.addAction("left rotation")
self._action_left.setIcon(QIcon(":/image/rotate_left.png"))
QObject.connect(self._action_left, SIGNAL("triggered(bool)"),
self.rotate_left)
# QWidgetAction : "Rotation Right"
self._action_right = self._toolbar.addAction("right rotation")
self._action_right.setIcon(QIcon(":/image/rotate_right.png"))
QObject.connect(self._action_right, SIGNAL("triggered(bool)"),
self.rotate_right)
# QWidgetAction : "Add point"
self._action_add = self._toolbar.addAction("Add point")
self._action_add.setCheckable(True)
self._toolgroup.addAction(self._action_add)
self._action_add.setIcon(QIcon(":/image/add.png"))
# QWidgetAction : "Delete point"
self._action_delete = self._toolbar.addAction("Delete point")
self._action_delete.setCheckable(True)
self._toolgroup.addAction(self._action_delete)
self._action_delete.setIcon(QIcon(":/image/delete.png"))
################### palette ###################
self._palette_select = QComboBox()
self._toolbar.addWidget(self._palette_select)
for palname in palette_names:
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
################### slider ###################
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setRange(0, self._view.nb_slices() - 1)
QObject.connect(self._img_slider, SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea, self._bot_toolbar)
################### statusbar ###################
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.statusbar = self.statusBar()
self.statusbar.addPermanentWidget(self._lab_coord)
self.statusbar.addPermanentWidget(self._lab_xcoord)
self.statusbar.addPermanentWidget(self._lab_ycoord)
self.statusbar.addPermanentWidget(self._lab_zcoord)
self.statusbar.addPermanentWidget(self._lab_intens)
##############################################
#
# update GUI
#
##############################################
def update_pix(self):
"""
"""
pix = self._view.pixmap()
if pix is not None:
self._item.setPixmap(pix)
else:
print 'None pixmap'
#update points
ind = self._view.current_slice()
for point in self._points:
if point is not None:
pid, item, x, y, z, textid = point
visible = abs(z - ind) < 5
item.setVisible(visible)
col = QColor.fromHsv((pid * 10) % 360, 255, 255)
if visible:
sca = max(0., (5 - abs(z - ind)) / 5.)
if z == ind:
pen = QPen(QColor(255, 255, 255))
pen.setWidthF(2.)
item.setPen(pen)
textid.setVisible(True)
else:
pen = QPen(QColor(0, 0, 0))
pen.setWidthF(2.)
item.setPen(pen)
textid.setVisible(False)
else:
sca = 1.
tr = QTransform()
tr.scale(sca, sca)
item.setTransform(tr)
item.update()
def coordinates(self, (i, j, k)):
self._last_mouse_x, self._last_mouse_y, self._last_slice = i, j, k
self.fill_infos()
def __init__ (self, parent=None) :
QMainWindow.__init__(self, parent)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.axis = 2
#central label
self._im_view = PixmapStackView()
self._label = ScalableLabel()
self.setCentralWidget(self._label)
#mouse handling
self._label.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
QObject.connect(self._label,
SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._label,
SIGNAL("mouse_move"),
self.mouse_pressed)
#toolbar
QObject.connect(self.ui.action_close,
SIGNAL("triggered(bool)"),
self.close)
QObject.connect(self.ui.action_snapshot,
SIGNAL("triggered(bool)"),
self.snapshot)
QObject.connect(self.ui.action_rotate_left,
SIGNAL("triggered(bool)"),
self.rotate_left)
QObject.connect(self.ui.action_rotate_right,
SIGNAL("triggered(bool)"),
self.rotate_right)
#palette
self._palette_select = QComboBox()
self.ui.toolbar.addWidget(self._palette_select)
for palname in palette_names :
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
#axis
self._axis = QComboBox(self)
self.ui.toolbar.addWidget(self._axis)
self._axis.addItem("Z-axis")
self._axis.addItem("Y-axis")
self._axis.addItem("X-axis")
self.connect(self._axis, SIGNAL('currentIndexChanged(int)'), self.change_axis )
#slider
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setEnabled(False)
QObject.connect(self._img_slider,
SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea,self._bot_toolbar)
#statusbar
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.ui.statusbar.addPermanentWidget(self._lab_coord)
self.ui.statusbar.addPermanentWidget(self._lab_xcoord)
self.ui.statusbar.addPermanentWidget(self._lab_ycoord)
self.ui.statusbar.addPermanentWidget(self._lab_zcoord)
self.ui.statusbar.addPermanentWidget(self._lab_intens)
self.set_title("<"+str(self.viewer_count)+">")
SlideViewer.viewer_count += 1
class SlideViewer (QMainWindow) :
"""Display each image in a stack using a slider
A pure QWidget (instead of QMainWindow) is also available, see openalea.image.gui.slide_viewer_widget.
"""
viewer_count = 0
def __init__ (self, parent=None) :
QMainWindow.__init__(self, parent)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.axis = 2
#central label
self._im_view = PixmapStackView()
self._label = ScalableLabel()
self.setCentralWidget(self._label)
#mouse handling
self._label.setMouseTracking(True)
self._last_mouse_x = 0
self._last_mouse_y = 0
QObject.connect(self._label,
SIGNAL("mouse_press"),
self.mouse_pressed)
QObject.connect(self._label,
SIGNAL("mouse_move"),
self.mouse_pressed)
#toolbar
QObject.connect(self.ui.action_close,
SIGNAL("triggered(bool)"),
self.close)
QObject.connect(self.ui.action_snapshot,
SIGNAL("triggered(bool)"),
self.snapshot)
QObject.connect(self.ui.action_rotate_left,
SIGNAL("triggered(bool)"),
self.rotate_left)
QObject.connect(self.ui.action_rotate_right,
SIGNAL("triggered(bool)"),
self.rotate_right)
#palette
self._palette_select = QComboBox()
self.ui.toolbar.addWidget(self._palette_select)
for palname in palette_names :
self._palette_select.addItem(palname)
QObject.connect(self._palette_select,
SIGNAL("currentIndexChanged(int)"),
self.palette_name_changed)
#axis
self._axis = QComboBox(self)
self.ui.toolbar.addWidget(self._axis)
self._axis.addItem("Z-axis")
self._axis.addItem("Y-axis")
self._axis.addItem("X-axis")
self.connect(self._axis, SIGNAL('currentIndexChanged(int)'), self.change_axis )
#slider
self._bot_toolbar = QToolBar("slider")
self._img_slider = QSlider(Qt.Horizontal)
self._img_slider.setEnabled(False)
QObject.connect(self._img_slider,
SIGNAL("valueChanged(int)"),
self.slice_changed)
self._bot_toolbar.addWidget(self._img_slider)
self.addToolBar(Qt.BottomToolBarArea,self._bot_toolbar)
#statusbar
self._lab_coord = QLabel("coords:")
self._lab_xcoord = QLabel("% 4d" % 0)
self._lab_ycoord = QLabel("% 4d" % 0)
self._lab_zcoord = QLabel("% 4d" % 0)
self._lab_intens = QLabel("intens: None")
self.ui.statusbar.addPermanentWidget(self._lab_coord)
self.ui.statusbar.addPermanentWidget(self._lab_xcoord)
self.ui.statusbar.addPermanentWidget(self._lab_ycoord)
self.ui.statusbar.addPermanentWidget(self._lab_zcoord)
self.ui.statusbar.addPermanentWidget(self._lab_intens)
self.set_title("<"+str(self.viewer_count)+">")
SlideViewer.viewer_count += 1
##############################################
#
# update GUI
#
##############################################
def update_pix (self) :
pix = self._im_view.pixmap()
if pix is not None :
self._label.setPixmap(pix)
def get_pixel_value_str(self, img, x, y, z):
px = img[x,y,z]
if isinstance(px, np.ndarray):
return str(px)
else:
return "%3d"%px
def fill_infos (self) :
x,y = self._label.pixmap_coordinates(self._last_mouse_x,
self._last_mouse_y)
img = self._im_view.image()
if img is not None :
i,j,k = self._im_view.data_coordinates(x,y)
self._lab_xcoord.setText("% 4d" % i)
self._lab_ycoord.setText("% 4d" % j)
self._lab_zcoord.setText("% 4d" % k)
imax,jmax,kmax = img.shape[:3]
if self.axis==0 : #axis x
if 0 <= i < jmax and 0 <= j < kmax and 0 <= k < imax :
self._lab_intens.setText("intens: %s" % self.get_pixel_value_str(img,k,i,j))
else :
self._lab_intens.setText("intens: None")
elif self.axis==1 : #axis y
if 0 <= i < imax and 0 <= j < kmax and 0 <= k < jmax :
self._lab_intens.setText("intens: %s" % self.get_pixel_value_str(img,i,k,j))
else :
self._lab_intens.setText("intens: None")
else : #axis z
if 0 <= i < imax and 0 <= j < jmax and 0 <= k < kmax :
self._lab_intens.setText("intens: %s" % self.get_pixel_value_str(img,i,j,k))
else :
self._lab_intens.setText("intens: None")
##############################################
#
# accessors
#
##############################################
def set_image (self, img) :
self._im_view.set_image(img)
try :
self.resolution = img.resolution[:]
except AttributeError :
pass
self._img_slider.setRange(0,self._im_view.nb_slices() - 1)
self._img_slider.setEnabled(True)
self.slice_changed(self._img_slider.value() )
def set_palette (self, palette, palette_name = None) :
if palette_name is not None :
ind = self._palette_select.findText(palette_name)
self._palette_select.setCurrentIndex(ind)
self._im_view.set_palette(palette,self.axis)
self.update_pix()
def set_title(self, title=None):
if title is not None :
self.setWindowTitle(title)
def change_axis(self,ind):
self.axis = 2-ind
try :
res = list(self.resolution)
del res[self.axis]
tr = self._im_view._transform
if tr % 180 :
self._label._resolution=res[1],res[0]
else :
self._label.set_resolution(*res)
except AttributeError :
pass
self._im_view._reconstruct_pixmaps(self.axis)
self._img_slider.setRange(0,self._im_view.nb_slices() - 1)
self._img_slider.setEnabled(True)
self.update_pix()
#self.fill_infos()
##############################################
#
# slots
#
##############################################
def palette_name_changed (self, palette_index) :
palname = str(self._palette_select.currentText() )
img = self._im_view.image()
if img is not None :
self.set_palette(palette_factory(str(palname),img.max()) )
def slice_changed (self, ind) :
self._im_view.set_current_slice(ind)
self.update_pix()
self.fill_infos()
def snapshot (self) :
"""write the current image
"""
pix = self._im_view.pixmap()
if pix is not None :
pix.save("slice%.4d.png" % self._img_slider.value() )
def wheelEvent (self, event) :
inc = event.delta() / 8 / 15
self._img_slider.setValue(self._img_slider.value() + inc)
def rotate_left (self) :
res=self._label._resolution
self._label._resolution=res[1],res[0]
self._im_view.rotate(-1)
self.update_pix()
def rotate_right (self) :
res=self._label._resolution
self._label._resolution=res[1],res[0]
self._im_view.rotate(1)
self.update_pix()
def mouse_pressed (self, event) :
self._last_mouse_x = event.x()
self._last_mouse_y = event.y()
self.fill_infos()
