class PixelSpace(ImageView):
def __init__(self, *args, **kwargs):
# Add axes
self.axesItem = PlotItem()
self.axesItem.axes["left"]["item"].setZValue(10)
self.axesItem.axes["top"]["item"].setZValue(10)
if "view" not in kwargs:
kwargs["view"] = self.axesItem
self._transform = QTransform()
self._raw_image = None
super(PixelSpace, self).__init__(*args, **kwargs)
self.imageItem.sigImageChanged.connect(self.updateAxes)
def transform(self, img=None):
# Build Quads
shape = img.shape
a = [(0, shape[-2] - 1), (shape[-1] - 1, shape[-2] - 1), (shape[-1] - 1, 0), (0, 0)]
b = [(0, 1), (shape[-1] - 1, 1), (shape[-1] - 1, shape[-2]), (0, shape[-2])]
quad1 = QPolygonF()
quad2 = QPolygonF()
for p, q in zip(a, b):
quad1.append(QPointF(*p))
quad2.append(QPointF(*q))
transform = QTransform()
QTransform.quadToQuad(quad1, quad2, transform)
for item in self.view.items:
if isinstance(item, ImageItem):
item.setTransform(transform)
self._transform = transform
return img, transform
def setImage(self, img, *args, **kwargs):
if img is None:
return
if getattr(self, "displaymode", DisplayMode.raw) == DisplayMode.raw:
self._raw_image = img
if not kwargs.get("transform", None):
img, transform = self.transform(img)
self.updateAxes()
super(PixelSpace, self).setImage(img, *args, transform=transform, **kwargs)
else:
super(PixelSpace, self).setImage(img, *args, **kwargs)
def setTransform(self):
self.setImage(self._raw_image) # this should loop back around to the respective transforms
def updateAxes(self):
self.axesItem.setLabel("bottom", "x (px)") # , units='s')
self.axesItem.setLabel("left", "z (px)")
class XArrayView(ImageView):
def __init__(self, *args, **kwargs):
# Add axes
self.axesItem = PlotItem()
self.axesItem.axes["left"]["item"].setZValue(10)
self.axesItem.axes["top"]["item"].setZValue(10)
if "view" not in kwargs:
kwargs["view"] = self.axesItem
super(XArrayView, self).__init__(*args, **kwargs)
self.view.invertY(False)
def setImage(self, img, **kwargs):
if hasattr(img, 'coords'):
if 'transform' not in kwargs:
xvals = img.coords[img.dims[-2]]
yvals = img.coords[img.dims[-1]]
xmin = float(xvals.min())
xmax = float(xvals.max())
ymin = float(yvals.min())
ymax = float(yvals.max())
# Position the image according to coords
shape = img.shape
a = [(0, shape[-2]), (shape[-1] - 1, shape[-2]),
(shape[-1] - 1, 1), (0, 1)]
b = [(ymin, xmin), (ymax, xmin), (ymax, xmax), (ymin, xmax)]
quad1 = QPolygonF()
quad2 = QPolygonF()
for p, q in zip(a, b):
quad1.append(QPointF(*p))
quad2.append(QPointF(*q))
transform = QTransform()
QTransform.quadToQuad(quad1, quad2, transform)
kwargs['transform'] = transform
if 'xvals' not in kwargs:
kwargs['xvals'] = np.asarray(img.coords[img.dims[0]])
# Set the timeline axis label from dims
self.ui.roiPlot.setLabel('bottom', img.dims[0])
# Label the image axes
self.axesItem.setLabel('left', img.dims[-2])
self.axesItem.setLabel('bottom', img.dims[-1])
# Add a bit more size
self.ui.roiPlot.setMinimumSize(QSize(0, 70))
# Bind coords from the xarray to the timeline axis
super(XArrayView, self).setImage(img, **kwargs)
def updateImage(self, autoHistogramRange=True):
if hasattr(self.image, 'dims'):
## Redraw image on screen
if self.image is None:
return
image = self.getProcessedImage()
if autoHistogramRange:
self.ui.histogram.setHistogramRange(self.levelMin,
self.levelMax)
# Transpose image into order expected by ImageItem
if self.imageItem.axisOrder == 'col-major':
axorder = ['t', 'x', 'y', 'c']
else:
axorder = ['t', 'y', 'x', 'c']
axorder = [
self.axes[ax] for ax in axorder if self.axes[ax] is not None
]
ax_swap = [image.dims[ax_index] for ax_index in axorder]
image = image.transpose(*ax_swap)
# Select time index
if self.axes['t'] is not None:
self.ui.roiPlot.show()
image = image[self.currentIndex]
self.imageItem.updateImage(np.asarray(image))
else:
super(XArrayView, self).updateImage(autoHistogramRange)
def quickMinMax(self, data):
"""
Estimate the min/max values of *data* by subsampling. MODIFIED TO USE THE 99TH PERCENTILE instead of max.
"""
if data is None:
return 0, 0
sl = slice(None, None, max(1, int(data.size // 1e6)))
data = np.asarray(data[sl])
levels = (np.nanmin(data),
np.nanpercentile(
np.where(data < np.nanmax(data), data, np.nanmin(data)),
99))
return [levels]
class SAXSViewerPlugin(DynImageView, QWidgetPlugin):
def __init__(self,
header: NonDBHeader = None,
field: str = 'primary',
toolbar: QToolBar = None,
*args,
**kwargs):
# Add q axes
self.axesItem = PlotItem()
self.axesItem.setLabel('bottom', u'q (Å⁻¹)') # , units='s')
self.axesItem.setLabel('left', u'q (Å⁻¹)')
self.axesItem.axes['left']['item'].setZValue(10)
self.axesItem.axes['top']['item'].setZValue(10)
if 'view' not in kwargs: kwargs['view'] = self.axesItem
super(SAXSViewerPlugin, self).__init__(**kwargs)
self.axesItem.invertY(False)
# Setup axes reset button
self.resetAxesBtn = QPushButton('Reset Axes')
sizePolicy = QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(1)
sizePolicy.setHeightForWidth(
self.resetAxesBtn.sizePolicy().hasHeightForWidth())
self.resetAxesBtn.setSizePolicy(sizePolicy)
self.resetAxesBtn.setObjectName("resetAxes")
self.ui.gridLayout.addWidget(self.resetAxesBtn, 2, 1, 1, 1)
self.resetAxesBtn.clicked.connect(self.autoRange)
# Setup LUT reset button
self.resetLUTBtn = QPushButton('Reset LUT')
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(1)
sizePolicy.setHeightForWidth(
self.resetLUTBtn.sizePolicy().hasHeightForWidth())
# self.resetLUTBtn.setSizePolicy(sizePolicy)
# self.resetLUTBtn.setObjectName("resetLUTBtn")
self.ui.gridLayout.addWidget(self.resetLUTBtn, 3, 1, 1, 1)
self.resetLUTBtn.clicked.connect(self.autoLevels)
# Hide ROI button and rearrange
self.ui.roiBtn.setParent(None)
self.ui.gridLayout.addWidget(self.ui.menuBtn, 1, 1, 1, 1)
self.ui.gridLayout.addWidget(self.ui.graphicsView, 0, 0, 3, 1)
# Setup coordinates label
self.coordinatesLbl = QLabel('--COORDINATES WILL GO HERE--')
self.ui.gridLayout.addWidget(self.coordinatesLbl,
3,
0,
1,
1,
alignment=Qt.AlignHCenter)
# Setup mask layer
self.maskimage = pg.ImageItem(opacity=.25)
self.view.addItem(self.maskimage)
# Setup calibration layer
self.calibrantimage = pg.ImageItem(opacity=.25)
self.view.addItem(self.calibrantimage)
# Empty ROI for later use
self.maskROI = pg.PolyLineROI([],
closed=True,
movable=False,
pen=pg.mkPen(color='r', width=2))
self.maskROI.handlePen = pg.mkPen(color='r', width=2)
self.maskROI.handleSize = 10
self.view.addItem(self.maskROI)
# Connect toolbar handlers
self.toolbar = toolbar
if self.toolbar:
self.toolbar.modegroup.triggered.connect(self.redraw)
# Setup results cache
self.results = []
# Set header
if header: self.setHeader(header, field)
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage(
'Header object contained no frames with field '
'{field}'
'.', msg.ERROR)
if data:
kwargs['transform'] = QTransform(0, -1, 1, 0, 0, data.shape[-2])
super(SAXSViewerPlugin, self).setImage(img=data, *args, **kwargs)
def setMaskImage(self, mask):
if mask is not None:
self.maskimage.setImage(mask,
lut=np.array([[0, 0, 0, 0],
[255, 0, 0, 255]]))
self.maskimage.setTransform(
QTransform(0, -1, 1, 0, 0, mask.shape[-2]))
else:
self.maskimage.clear()
def setCalibrantImage(self, data):
if data is not None:
self.calibrantimage.setImage(data, lut=calibrantlut)
self.calibrantimage.setTransform(QTransform(0, 1, 1, 0, 0, 0))
else:
self.calibrantimage.clear()
def redraw(self):
if not self.parent().currentWidget() == self:
return # Don't redraw when not shown
for result in self.results:
try:
if self.toolbar.cakeaction.isChecked():
self.setImage(result['cake'].value)
break
elif self.toolbar.remeshaction.isChecked():
self.setImage(result['remesh'].value
) # TODO: add checkbox to toolbar
break
elif 'inpaint' in result:
self.setImage(result['inpaint'].value)
break
except TypeError:
continue
else: # if self.toolbar.rawaction.isChecked():
self.setHeader(self.header, self.field)
def setResults(self, results):
self.results = results
self.redraw()
class EFIViewerPlugin(Crosshair, QCoordinates, DynImageView, QWidgetPlugin):
def __init__(self,
header: NonDBHeader = None,
field: str = 'primary',
toolbar: QToolBar = None,
*args,
**kwargs):
# Add axes
self.axesItem = PlotItem()
# self.axesItem.setLabel('bottom', u'q ()') # , units='s')
# self.axesItem.setLabel('bottom', u'q ()') # , units='s')
# self.axesItem.setLabel('left', u'q ()')
self.axesItem.axes['left']['item'].setZValue(10)
self.axesItem.axes['top']['item'].setZValue(10)
if 'view' not in kwargs: kwargs['view'] = self.axesItem
super(EFIViewerPlugin, self).__init__(**kwargs)
self.axesItem.invertY(True)
# Setup axes reset button
self.resetAxesBtn = QPushButton('Reset Axes')
sizePolicy = QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(1)
sizePolicy.setHeightForWidth(
self.resetAxesBtn.sizePolicy().hasHeightForWidth())
self.resetAxesBtn.setSizePolicy(sizePolicy)
self.resetAxesBtn.setObjectName("resetAxes")
self.ui.gridLayout.addWidget(self.resetAxesBtn, 2, 1, 1, 1)
self.resetAxesBtn.clicked.connect(self.autoRange)
# Setup LUT reset button
self.resetLUTBtn = QPushButton('Reset LUT')
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(1)
sizePolicy.setHeightForWidth(
self.resetLUTBtn.sizePolicy().hasHeightForWidth())
# self.resetLUTBtn.setSizePolicy(sizePolicy)
# self.resetLUTBtn.setObjectName("resetLUTBtn")
self.ui.gridLayout.addWidget(self.resetLUTBtn, 3, 1, 1, 1)
self.resetLUTBtn.clicked.connect(self.autoLevels)
# Hide ROI button and rearrange
# self.ui.roiBtn.setParent(None)
# self.ui.gridLayout.addWidget(self.ui.menuBtn, 1, 1, 1, 1)
# self.ui.gridLayout.addWidget(self.ui.graphicsView, 0, 0, 3, 1)
# Setup coordinates label
# self.coordinatesLbl = QLabel('--COORDINATES WILL GO HERE--')
# self.ui.gridLayout.addWidget(self.coordinatesLbl, 3, 0, 1, 1, alignment=Qt.AlignHCenter)
# Set header
if header: self.setHeader(header, field)
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage(
f'Header object contained no frames with field {field}.',
msg.ERROR)
for ii in header:
msg.logMessage('header types = '.format(type(ii)))
if data:
# data = np.squeeze(data) #test for 1D spectra
if data.ndim > 1:
# kwargs['transform'] = QTransform(0, -1, 1, 0, 0, data.shape[-2])
# NOTE PAE: for setImage:
# use setImage(xVals=timeVals) to set the values on the slider for 3D data
try:
# Retrieve the metadata for pixel scale and units
descriptorsTee = itertools.tee(
header.descriptors,
1)[0] # tee the descriptors generator once
_ = next(descriptorsTee) # start document
headerTitle, md = next(
descriptorsTee) # descriptor document with metadata
scale0 = (md['PhysicalSizeX'], md['PhysicalSizeY'])
units0 = (md['PhysicalSizeXUnit'], md['PhysicalSizeYUnit'])
except:
scale0 = (1, 1)
units0 = ('', '')
msg.logMessage(
'EFIviewer: No pixel size or units detected')
super(EFIViewerPlugin, self).setImage(img=data,
scale=scale0,
*args,
**kwargs)
self.axesItem.setLabel('bottom', text='X', units=units0[0])
self.axesItem.setLabel('left', text='Y', units=units0[1])
