def drawROI(self):
# Custom ROI for selecting an image region
handle1_x = self.win.rois[0].getLocalHandlePositions()[0][1].x()
handle1_y = self.win.rois[0].getLocalHandlePositions()[0][1].y()
handle2_x = self.win.rois[0].getLocalHandlePositions()[1][1].x()
handle2_y = self.win.rois[0].getLocalHandlePositions()[1][1].y()
#imageHeight = self.win.imageDimensions()[1]
#angle = math.degrees(math.atan2(handle2_y-handle1_y , handle2_x-handle1_x))
def newY(handle1_y, handle2_y):
diff = abs(handle1_y - handle2_y)
if handle2_y - handle1_y >= 0:
return handle1_y - diff
else:
return handle1_y + diff
self.roi = pg.LineROI(
[handle1_x, handle1_y],
[handle2_x, newY(handle1_y, handle2_y)],
width=self.width,
pen=(1, 9))
#roi.addScaleHandle([0.5, 1], [0.5, 0.5])
#roi.addScaleHandle([0, 0.5], [0.5, 0.5])
self.win.removeAllROIs()
self.win.imageview.addItem(self.roi)
def setROI(self, shape):
make = [pg.LineROI, pg.RectROI]
roi = None
if shape == 0:
roi = pg.LineROI([0, 60], [20, 80], width=1, pen=(1, 9))
elif shape == 1:
roi = pg.RectROI([20, 20], [20, 20], pen=(0, 9))
else:
roi = pg.CircleROI([80, 50], [20, 20], pen=(4, 9))
self.rois.append(roi)
self.view.addItem(roi)
def test_LineROI_coords(p1, p2):
pw = pg.plot()
lineroi = pg.LineROI(p1, p2, width=0.5, pen="r")
pw.addItem(lineroi)
# first two handles are the scale-rotate handles positioned by pos1, pos2
for expected, (name, scenepos) in zip([p1, p2],
lineroi.getSceneHandlePositions()):
got = lineroi.mapSceneToParent(scenepos)
assert math.isclose(got.x(), expected[0])
assert math.isclose(got.y(), expected[1])
label1 = w1.addLabel(text, row=0, col=0)
v1a = w1.addViewBox(row=1, col=0, lockAspect=True)
v1b = w1.addViewBox(row=2, col=0, lockAspect=True)
img1a = pg.ImageItem(arr)
v1a.addItem(img1a)
img1b = pg.ImageItem()
v1b.addItem(img1b)
v1a.disableAutoRange('xy')
v1b.disableAutoRange('xy')
v1a.autoRange()
v1b.autoRange()
rois = []
rois.append(pg.RectROI([20, 20], [20, 20], pen=(0, 9)))
rois[-1].addRotateHandle([1, 0], [0.5, 0.5])
rois.append(pg.LineROI([0, 60], [20, 80], width=5, pen=(1, 9)))
rois.append(
pg.MultiRectROI([[20, 90], [50, 60], [60, 90]], width=5, pen=(2, 9)))
rois.append(pg.EllipseROI([60, 10], [30, 20], pen=(3, 9)))
rois.append(pg.CircleROI([80, 50], [20, 20], pen=(4, 9)))
#rois.append(pg.LineSegmentROI([[110, 50], [20, 20]], pen=(5,9)))
rois.append(
pg.PolyLineROI([[80, 60], [90, 30], [60, 40]], pen=(6, 9), closed=True))
def update(roi):
img1b.setImage(roi.getArrayRegion(arr, img1a), levels=(0, arr.max()))
v1b.autoRange()
for roi in rois:
def setup(self):
self.settings.New('drift_correct_type',
dtype=str,
initial='Pairwise',
choices=('Pairwise', 'Pairwise + Running Avg'))
self.settings.New('drift_correct_adc_chan', dtype=int)
self.settings.New('drift_correct', dtype=bool)
self.settings.New('overwrite_alignment', dtype=bool)
# if drift corrected datasets already exist, overwrite?
self.settings.New('run_preprocess', dtype=bool)
self.settings.get_lq('run_preprocess').add_listener(self.preprocess)
self.settings.New('use_preprocess', dtype=bool, initial=True)
self.settings.get_lq('use_preprocess').add_listener(self.load_new_data)
self.settings.New('update_auger_map', dtype=bool, initial=False)
self.settings.get_lq('update_auger_map').add_listener(
self.update_current_auger_map)
self.settings.New('equalize_detectors', dtype=bool)
self.settings.New('normalize_by_pass_energy', dtype=bool)
self.settings.New('spatial_smooth_sigma', dtype=float, vmin=0.0)
self.settings.New('spectral_smooth_type',
dtype=str,
choices=['None', 'Gaussian', 'Savitzky-Golay'],
initial='None')
self.settings.New('spectral_smooth_gauss_sigma', dtype=float, vmin=0.0)
self.settings.New('spectral_smooth_savgol_width', dtype=int, vmin=0)
self.settings.New('spectral_smooth_savgol_order',
dtype=int,
vmin=0,
initial=2)
# Assume same tougaard parameters everywhere
self.settings.New('subtract_tougaard', dtype=bool)
self.settings.New('R_loss', dtype=float)
self.settings.New('E_loss', dtype=float)
auger_lqs = [
'equalize_detectors', 'normalize_by_pass_energy',
'spatial_smooth_sigma', 'spectral_smooth_type',
'spectral_smooth_gauss_sigma', 'spectral_smooth_savgol_width',
'spectral_smooth_savgol_order', 'subtract_tougaard', 'R_loss',
'E_loss'
]
# Link all the auger spectrum lqs to the update current auger map listener
for alq in auger_lqs:
self.settings.get_lq(alq).add_listener(
self.update_current_auger_map)
self.settings.New('ke0_start', dtype=float)
self.settings.New('ke0_stop', dtype=float)
self.settings.New('ke1_start', dtype=float)
self.settings.New('ke1_stop', dtype=float)
for lqname in ['ke0_start', 'ke0_stop', 'ke1_start', 'ke1_stop']:
self.settings.get_lq(lqname).add_listener(
self.on_change_ke_settings)
# Subtract the B section (ke1_start through ke1_stop) by a power law fit
self.settings.New('subtract_ke1',
dtype=str,
choices=['None', 'Linear', 'Power Law'],
initial='None')
self.settings.get_lq('subtract_ke1').add_listener(
self.update_current_auger_map)
#Math mode now updates automatically on change
self.settings.New('math_mode', dtype=str, initial='A')
self.settings.get_lq('math_mode').add_listener(
self.on_change_math_mode)
self.settings.New('AB_mode',
dtype=str,
choices=['Mean', 'Integral'],
initial='Mean')
self.settings.get_lq('AB_mode').add_listener(
self.on_change_ke_settings)
self.settings.New('spectrum_over_ROI', dtype=bool)
self.settings.get_lq('spectrum_over_ROI').add_listener(
self.on_change_spectrum_over_ROI)
self.settings.New('analysis_over_spectrum', dtype=bool)
self.settings.get_lq('analysis_over_spectrum').add_listener(
self.update_current_auger_map)
self.settings.New('mean_spectrum_only', dtype=bool, initial=False)
self.settings.get_lq('mean_spectrum_only').add_listener(
self.on_change_mean_spectrum_only)
# Make plots on white background
#pg.setConfigOption('background', 'w')
#pg.setConfigOption('foreground', 'k')
self.ui = self.dockarea = dockarea.DockArea()
# List of settings to include in preprocessing tab
names_prep = [
'drift_correct_type', 'drift_correct_adc_chan', 'drift_correct',
'overwrite_alignment', 'run_preprocess'
]
self.setdock = self.dockarea.addDock(
name='Settings',
position='left',
widget=self.settings.New_UI(exclude=names_prep))
self.prepdock = self.dockarea.addDock(
name='Preprocess',
position='left',
widget=self.settings.New_UI(include=names_prep))
self.dockarea.moveDock(self.setdock, 'above', self.prepdock)
# Images
self.imview_sem0_stack = pg.ImageView()
self.imview_sem0_stack.getView().invertY(False) # lower left origin
self.imdockA_stack = self.dockarea.addDock(
name='SE2 Image Stack', widget=self.imview_sem0_stack)
self.imview_sem1_stack = pg.ImageView()
self.imview_sem1_stack.getView().invertY(False) # lower left origin
self.imdockB_stack = self.dockarea.addDock(
name='InLens Image Stack',
position='right',
widget=self.imview_sem1_stack)
self.imview_sem0 = pg.ImageView()
self.imview_sem0.getView().invertY(False) # lower left origin
self.imdockA = self.dockarea.addDock(name='SE2 Mean Image',
widget=self.imview_sem0)
self.imview_sem1 = pg.ImageView()
self.imview_sem1.getView().invertY(False) # lower left origin
self.imdockB = self.dockarea.addDock(name='InLens Mean Image',
widget=self.imview_sem1)
self.imview_auger = pg.ImageView()
self.imview_auger.getView().invertY(False) # lower left origin
self.imdockAuger = self.dockarea.addDock(name='Auger Map',
widget=self.imview_auger)
self.im_auger = self.imview_auger.getImageItem()
# tab image and auger map docks
self.dockarea.moveDock(self.imdockA_stack, 'above', self.imdockB_stack)
self.dockarea.moveDock(self.imdockB, 'above', self.imdockA_stack)
self.dockarea.moveDock(self.imdockA, 'above', self.imdockB)
self.dockarea.moveDock(self.imdockAuger, 'above', self.imdockA)
# Polygon ROI
self.poly_roi = pg.PolyLineROI([[20, 0], [20, 20], [0, 20]],
pen=pg.mkPen((255, 0, 0),
dash=[5, 5],
width=1.5),
closed=True)
#self.poly_roi = pg.RectROI([20, 20], [20, 20], pen=(0,9))
#self.poly_roi = pg.CircleROI((0,0), (10,10) , movable=True, pen=(0,9))
#self.poly_roi.addTranslateHandle((0.5,0.5))
self.imview_auger.getView().addItem(self.poly_roi)
self.poly_roi.sigRegionChanged[object].connect(self.on_change_roi)
# Scalebar ROI
self.scalebar = pg.LineROI([5, 5], [25, 5],
width=0,
pen=pg.mkPen(color=(255, 255, 0),
width=4.5))
self.imview_auger.getView().addItem(self.scalebar)
# Create initial scalebar w/ text
self.scale_text = pg.TextItem(color=(255, 255, 0), anchor=(0.5, 1))
self.imview_auger.getView().addItem(self.scale_text)
self.scale_text.setFont(pg.QtGui.QFont('Arial', pointSize=11))
self.scalebar.sigRegionChanged[object].connect(self.on_change_scalebar)
# Change handle colors so they don't appear by default, but do when hovered over
scale_handles = self.scalebar.getHandles()
scale_handles[0].currentPen.setColor(pg.mkColor(255, 255, 255, 0))
scale_handles[1].currentPen.setColor(pg.mkColor(255, 255, 255, 0))
# This disables the middle handle that allows line width change
scale_handles[2].setOpacity(0.0)
# Spectrum plot
self.graph_layout = pg.GraphicsLayoutWidget()
self.spec_plot = self.graph_layout.addPlot()
self.legend = self.spec_plot.addLegend()
self.spec_plot.setLabel('bottom', 'Electron Kinetic Energy')
self.spec_plot.setLabel('left', 'Intensity (Hz)')
#self.rect_plotdata = self.spec_plot.plot()
#self.point_plotdata = self.spec_plot.plot(pen=(0,9))
self.dockarea.addDock(name='Spec Plot',
position='bottom',
widget=self.graph_layout)
self.lr0 = pg.LinearRegionItem(values=[0, 1],
brush=QtGui.QBrush(
QtGui.QColor(0, 0, 255, 50)))
self.lr1 = pg.LinearRegionItem(values=[2, 3],
brush=QtGui.QBrush(
QtGui.QColor(255, 0, 0, 50)))
for lr in (self.lr0, self.lr1):
lr.setZValue(10)
self.spec_plot.addItem(lr, ignoreBounds=True)
lr.sigRegionChangeFinished.connect(self.on_change_regions)
self.chan_plotlines = []
# define plotline color scheme going from orange -> yellow -> green
R = np.linspace(220, 0, 4)
G = np.linspace(220, 100, 4)
plot_colors = [(R[0], G[0], 0), (R[1], G[0], 0), (R[0], G[1], 0),
(R[2], G[0], 0), (R[0], G[2], 0), (R[3], G[0], 100),
(R[0], G[3], 0)]
for ii in range(7):
self.chan_plotlines.append(
self.spec_plot.plot([0],
pen=pg.mkPen(color=plot_colors[ii],
width=2),
name='chan ' + str(ii),
width=20))
self.total_plotline = self.spec_plot.plot(pen=pg.mkPen(color=(0, 0, 0),
width=3),
name='mean')
def setROI(self, shape, rect=((10, 10), (20, 20))):
'''ROI 추가를 위한 메서드. 좌상, 우하 좌표와, 모양을 인자로 받아
선형, 사각형, 다선형, 삼각형, 원형의 ROI를 추가한다'''
make = [pg.LineROI, pg.RectROI]
roi_lst = []
roi_id = len(self.roi_lst)
def update(roi):
'''ROI에 변화가 생겼을 대에 이를 다른 뷰에 적용시킨다'''
state = roi.saveState()
for r in self.roi_lst[roi_id]:
r.setAngle(state['angle'], update=False)
r.setPos(state['pos'], update=False)
r.setSize(state['size'], update=False)
def clicked(roi):
'''ROI 우클릭 시에 팝업 윈도우를 보여준다'''
ROIPopup(roi, self.ui)
print "clicked"
(x1, y1), (x2, y2) = rect
x = min(x1, x2)
y = min(y1, y2)
xlen = abs(x1 - x2)
ylen = abs(y1 - y2)
for widget in self.widget_lst:
if shape == 0:
roi = pg.LineROI([x1, y1], [x2, 2 * y1 - y2],
width=0,
pen=(1, 9))
elif shape == 1:
roi = pg.RectROI([x, y], [xlen, ylen], pen=(3, 9))
elif shape == 2:
roi = pg.PolyLineROI(
[[x, y + ylen], [x + xlen / 4, y], [
x + xlen / 2, y + ylen
], [x + xlen * 3 / 4, y], [x + xlen, y + ylen]],
closed=False,
pen=(5, 9))
elif shape == 3:
roi = pg.PolyLineROI(
[[x, y], [x + xlen / 4, y + ylen], [x + xlen / 2, y],
[x + xlen * 3 / 4, y + ylen], [x + xlen, y]],
closed=False,
pen=(7, 9))
elif shape == 4:
roi = pg.PolyLineROI(
[[x, y], [x + xlen / 2, y + ylen], [x + xlen, y]],
closed=True,
pen=(9, 9))
elif shape == 5:
roi = pg.EllipseROI([x, y], [xlen, ylen], pen=(4, 9))
else:
raise Exception("Shape unbound")
# 시그널 연결
roi.sigRegionChanged.connect(update)
roi.setAcceptedMouseButtons(QtCore.Qt.RightButton)
roi.sigClicked.connect(clicked)
if shape == 2 or shape == 3 or shape == 4:
for seg in roi.segments:
seg.sigRegionChanged.connect(update)
widget.addItem(roi)
roi_lst.append(roi)
self.roi_lst.append(roi_lst)
return x
#win.addWindow(map1)
#ui.graphicsView.useOpenGL()
vb = pg.ViewBox()
ui.graphicsView.setCentralItem(vb)
vb.setAspectLocked()
img = pg.ImageItem()
vb.addItem(img)
## ROI setting
rois = []
# add default roi
for i in [0, 1, 2, 3]:
y0 = 70 + i * 30
rois.append(pg.RectROI([400, y0], [20, 20]))
vb.addItem(rois[i])
bg = pg.LineROI([0, 0], [0, -200], width=5)
vb.addItem(bg)
# camera2c Player
ptr = 0
lastTime = ptime.time()
fps = None
def update():
global ui, ptr, lastTime, fps, img
# Transfer the orign postion and color of ROI and edge
if ui.pushButton_roi.isChecked():
wormmap = np.zeros((4, 6))
for i in [0, 1, 2, 3]:
