def test_get_arr2d():
""" Series.get_arr2d """
series = Series(hdf5, cachedir=cache)
arr2d = series.get_arr2d(100, 3, axis='xy')
assert arr2d.shape == shape[0:2]
arr2d = series.get_arr2d(100, 20, axis='yz')
assert arr2d.shape == (shape[0], shape[2])
arr2d = series.get_arr2d(100, 20, axis='xz')
assert arr2d.shape == (shape[1], shape[2])
class SimuViewer(QMainWindow, ControlPanel, HeatmapPanel, PointsPanel, Menu):
""" Main application window. """
def __init__(self, hdf5_path=None, parent=None):
# init position
self.position = {
'x': 0,
'y': 0,
'z': 0,
't': 0,
}
# init points
self.selected_points = set([])
# init window
QMainWindow.__init__(self, parent)
self.setWindowTitle('SimuViewer')
# create widgets
self.create_menu()
self.create_main_frame()
self.create_status_bar()
# load hdf5 file
if hdf5_path:
if os.path.exists(hdf5_path):
status = self.load_file(hdf5_path)
if isinstance(status, Exception):
raise IOError("Fail to open %s"%hdf5_path)
else:
raise IOError("%s not exist."%hdf5_path)
else:
# load hdf5 file from window
self.window_load_file()
def load_file(self, hdf5_path):
""" Load Series from hdf5 file """
try:
self.series = Series(hdf5_path)
return True
except Exception as e:
log.error(e)
return e
def save_plot(self):
""" Save current image """
file_choices = "PNG (*.png);;JPEG (*.jpg);;TIFF (*.tif);;ALL (*)"
path, _ = QFileDialog.getSaveFileName(self,
'Open file', 'image.png', file_choices)
if path:
self.canvas.print_figure(path, dpi=self.dpi)
log.info("Save image file to %s"%path)
def on_click(self, event):
"""
handle matplotlib.backend_bases.MouseEvent ('button_press_event')
collection clicked positions.
"""
t, z = self.position['t'], self.position['z']
x, y = event.xdata, event.ydata
if x and y:
msg = "You've clicked on (%.2f, %.2f, %.2f, %.2f)"%(t, x, y, z)
log.info(msg)
point = x_, y_, z_ = int(x), int(y), int(z)
if point not in self.selected_points:
self.selected_points.add(point)
self.points_list.addItem(str(point))
def on_motion(self, event):
"""
handle matplotlib.backend_bases.MouseEvent ('motion_notify_event')
refersh status_text
"""
x, y = event.xdata, event.ydata
if x and y and hasattr(self, 'series'):
mat = self.series.get_arr2d(self.position['t'],
self.position['z'],
axis='xy')
try:
value = mat[int(round(y)), int(round(x))]
except:
value = 0.0
text = "position: (%d, %.2f, %.2f, %d) value: %.2f"%(
self.position['t'], x, y,
self.position['z'], value)
if hasattr(self, 'heatmap2d') and self.heatmap_cb.isChecked():
pvalue = self.heatmap2d[int(round(y)), int(round(x))]
text += " pvalue: %f"%pvalue
self.status_text.setText(text)
def on_draw(self):
"""
Refresh the figure.
"""
if hasattr(self, 'series'):
# self.series exist,
# clear the axes and redraw the plot anew
#
self.axes.clear()
self.axes.grid(self.grid_cb.isChecked())
mat = self.series.get_arr2d(self.position['t'],
self.position['z'],
axis='xy')
self.axes.matshow(mat, cmap='gray')
if hasattr(self, 'heatmap') and self.heatmap_cb.isChecked():
from .heatmap import draw_heatmap
draw_heatmap(self.axes, self.heatmap2d, cutoff=self.heatmap_cutoff)
try:
self.canvas.draw()
except AttributeError as e:
self.axes.clear()
self.axes.grid(self.grid_cb.isChecked())
self.axes.matshow(mat, cmap='gray')
self.canvas.draw()
log.error(str(e))
else:
# self.series not exist
# show text
#
msg = "Data empty, please open one hdf5 file."
log.warning(msg)
self.axes.text(0.1, 0.5, msg,
bbox={'facecolor':'red', 'alpha':0.5, 'pad':10})
def on_refresh(self):
"""
Refresh whole frame.
"""
if hasattr(self, 'series'):
t_max = self.series.shape[0] - 1
z_max = self.series.shape[3] - 1
else:
t_max = 1
z_max = 1
self.slider_t.setRange(0, t_max)
self.slider_z.setRange(0, z_max)
self.on_draw()
def create_main_frame(self):
"""
Create main frame and manage the frame layout.
main_frame(QVBoxLayout)
-----------------------
canvas(FigureCanvas)
NavigationToolBar
control(QHBoxLayout)
points(QHBoxLayout)
"""
self.main_frame = QWidget()
# Create the mpl Figure and FigCanvas objects.
# 5x4 inches, 100 dots-per-inch
#
self.dpi = 100
self.fig = Figure((8, 6.4), dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self.main_frame)
# Since we have only one plot, we can use add_axes
# instead of add_subplot, but then the subplot
# configuration tool in the navigation toolbar wouldn't
# work.
#
self.axes = self.fig.add_subplot(111)
# Bind the events for mouse clicking and motion
#
self.canvas.mpl_connect('button_press_event', self.on_click)
self.canvas.mpl_connect('motion_notify_event', self.on_motion)
# Create the navigation toolbar, tied to the canvas
#
self.mpl_toolbar = NavigationToolbar(self.canvas, self.main_frame)
# Create control hbox
#
control_hbox = self.create_control_hbox()
# Create heatmap hbox
heatmap_hbox = self.create_heatmap_hbox()
# Create points hbox
#
points_hbox = self.create_points_hbox()
vbox = QVBoxLayout()
vbox.addWidget(self.mpl_toolbar)
vbox.addWidget(self.canvas)
vbox.addLayout(control_hbox)
vbox.addLayout(heatmap_hbox)
vbox.addLayout(points_hbox)
self.main_frame.setLayout(vbox)
self.setCentralWidget(self.main_frame)
def create_status_bar(self):
self.status_text = QLabel("position: value:")
self.statusBar().addWidget(self.status_text, 1)