/
widgets.py
1225 lines (992 loc) · 46.1 KB
/
widgets.py
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# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015, Vispy Development Team. All Rights Reserved.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
# -----------------------------------------------------------------------------
# vispy: gallery 2
#
# Adapted for use as a widget by Ron Pandolfi
# volumeViewer.getHistogram method borrowed from PyQtGraph
from collections import deque
import numpy as np
from functools import partial
from PySide import QtGui, QtCore
from vispy import scene # , app, io
from vispy.color import Colormap # , BaseColormap, ColorArray
from pipeline import loader
import pyqtgraph as pg
import imageio
import os
import fmanager
__author__ = "Ronald J Pandolfi"
__copyright__ = "Copyright 2016, CAMERA, LBL, ALS"
__credits__ = ["Ronald J Pandolfi", "Dinesh Kumar", "Singanallur Venkatakrishnan", "Luis Luque", "Alexander Hexemer"]
__license__ = ""
__version__ = "1.2.1"
__maintainer__ = "Ronald J Pandolfi"
__email__ = "ronpandolfi@lbl.gov"
__status__ = "Beta"
class TomoViewer(QtGui.QWidget):
"""
Class that holds projection, sinogram, recon preview, and process-settings viewers for a tomography dataset.
"""
sigReconFinished = QtCore.Signal()
def __init__(self, paths=None, data=None, *args, **kwargs):
if paths is None and data is None:
raise ValueError('Either data or path to file must be provided')
super(TomoViewer, self).__init__(*args, **kwargs)
self._recon_path = None
self.viewstack = QtGui.QStackedWidget(self)
self.viewmode = QtGui.QTabBar(self)
self.viewmode.addTab('Projection View') # TODO: Add icons!
self.viewmode.addTab('Sinogram View')
self.viewmode.addTab('Slice Preview')
self.viewmode.addTab('3D Preview')
self.viewmode.addTab('Reconstruction View')
self.viewmode.setShape(QtGui.QTabBar.TriangularSouth)
if data is not None:
self.data = data
elif paths is not None and len(paths):
self.data = self.loaddata(paths)
self.cor = float(self.data.shape[1])/2.0
self.projectionViewer = ProjectionViewer(self.data, center=self.cor, parent=self)
self.projectionViewer.centerBox.setRange(0, self.data.shape[1])
if fmanager.recon_function is not None:
center_param = fmanager.recon_function.params.child('center')
# Uncomment this if you want convenience of having the center parameter in pipeline connected to the
# manual center widget, but this limits the center options to a resolution of 0.5
# self.projectionViewer.sigCenterChanged.connect(
# lambda x: center_param.setValue(x)) #, blockSignal=center_param.sigValueChanged))
self.projectionViewer.setCenterButton.clicked.connect(
lambda: center_param.setValue(self.projectionViewer.centerBox.value()))
center_param.sigValueChanged.connect(lambda p,v: self.projectionViewer.centerBox.setValue(v))
center_param.sigValueChanged.connect(lambda p,v: self.projectionViewer.updateROIFromCenter(v))
self.viewstack.addWidget(self.projectionViewer)
self.sinogramViewer = StackViewer(loader.SinogramStack.cast(self.data), parent=self)
self.sinogramViewer.setIndex(self.sinogramViewer.data.shape[0] // 2)
self.viewstack.addWidget(self.sinogramViewer)
self.previewViewer = PreviewViewer(self.data.shape[1], parent=self)
self.viewstack.addWidget(self.previewViewer)
self.preview3DViewer = Preview3DViewer(paths=paths, data=data)
self.viewstack.addWidget(self.preview3DViewer)
self.reconstructionViewer = ReconstructionViewer(parent=self)
self.viewstack.addWidget(self.reconstructionViewer)
v = QtGui.QVBoxLayout(self)
v.setContentsMargins(0, 0, 0, 0)
v.addWidget(self.viewstack)
v.addWidget(self.viewmode)
self.setLayout(v)
self.viewmode.currentChanged.connect(self.currentChanged)
self.viewstack.currentChanged.connect(self.viewmode.setCurrentIndex)
@staticmethod
def loaddata(paths, raw=True):
if raw:
return loader.ProjectionStack(paths)
else:
return loader.StackImage(paths)
def getsino(self, slc=None): #might need to redo the flipping and turning to get this in the right orientation
if slc is None:
return np.ascontiguousarray(self.sinogramViewer.currentdata[:,np.newaxis,:])
else:
return np.ascontiguousarray(self.data.fabimage[slc])
def getproj(self, slc=None):
if slc is None:
return np.ascontiguousarray(self.projectionViewer.currentdata[np.newaxis, :, :])
else:
return np.ascontiguousarray(self.data.fabimage[slc])
def getflats(self, slc=None):
if slc is None:
return np.ascontiguousarray(self.data.flats[:, self.sinogramViewer.currentIndex, :])
else:
return np.ascontiguousarray(self.data.flats[slc])
def getdarks(self, slc=None):
if slc is None:
return np.ascontiguousarray(self.data.darks[: ,self.sinogramViewer.currentIndex, :])
else:
return np.ascontiguousarray(self.data.darks[slc]) #slice(*slc[0]), slice(*slc[1]), :])
def getheader(self):
return self.data.header
def currentChanged(self, index):
self.viewstack.setCurrentIndex(index)
def setCorValue(self, value):
self.cor = value
def runSlicePreview(self):
fmanager.run_preview_recon(*fmanager.pipeline_preview_action(self, self.addSlicePreview))
def run3DPreview(self):
slc = (slice(None), slice(None, None, 8), slice(None, None, 8))
fmanager.cor_scale = lambda x: x//8
fmanager.run_preview_recon(*fmanager.pipeline_preview_action(self, self.add3DPreview, slc=slc))
def runFullRecon(self, proj, sino, nchunk, ncore, update_call):
fmanager.run_full_recon(self, proj, sino, nchunk, ncore, update_call, self.fullReconFinished)
def addSlicePreview(self, params, recon):
self.previewViewer.addPreview(np.rot90(recon[0],1), params)
self.viewstack.setCurrentWidget(self.previewViewer)
def add3DPreview(self, params, recon):
# pad = int((recon.shape[1] - self.data.shape[1] // 8) / 2)
# if pad > 0:
# recon = recon[:, pad:-pad, pad:-pad]
recon = np.flipud(recon)
self.viewstack.setCurrentWidget(self.preview3DViewer)
self.preview3DViewer.setPreview(recon, params)
def fullReconFinished(self):
self.sigReconFinished.emit()
path = fmanager.get_output_path()
# if not extension was given assume it is a tiff directory.
if '.' not in path:
path = os.path.split(path)[0]
self.reconstructionViewer.openDataset(path=path)
self.viewstack.setCurrentWidget(self.reconstructionViewer)
def onManualCenter(self, active):
if active:
self.projectionViewer.showCenterDetection()
self.viewstack.setCurrentWidget(self.projectionViewer)
else:
self.projectionViewer.hideCenterDetection()
class ImageView(pg.ImageView):
"""
Subclass of PG ImageView to correct z-slider signal behavior, and add coordinate label.
"""
sigDeletePressed = QtCore.Signal()
def __init__(self, *args, **kwargs):
super(ImageView, self).__init__(*args, **kwargs)
self.scene.sigMouseMoved.connect(self.mouseMoved)
self.coordsLabel = QtGui.QLabel(' ', parent=self)
self.coordsLabel.setMinimumHeight(16)
self.layout().addWidget(self.coordsLabel)
self.coordsLabel.setAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignBottom)
self.setStyleSheet("background-color: rgba(0,0,0,0%)")
def buildMenu(self):
super(ImageView, self).buildMenu()
self.menu.removeAction(self.normAction)
def keyPressEvent(self, ev):
super(ImageView, self).keyPressEvent(ev)
if ev.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down):
self.timeLineChanged()
elif ev.key() == QtCore.Qt.Key_Delete or ev.key() == QtCore.Qt.Key_Backspace:
self.sigDeletePressed.emit()
def timeIndex(self, slider):
## Return the time and frame index indicated by a slider
if self.image is None:
return (0,0)
t = slider.value()
xv = self.tVals
if xv is None:
ind = int(t)
else:
if len(xv) < 2:
return (0,0)
totTime = xv[-1] + (xv[-1]-xv[-2])
inds = np.argwhere(xv <= t)
if len(inds) < 1:
return (0,t)
ind = inds[-1,0]
return ind, t
def mouseMoved(self, ev):
pos = ev
viewBox = self.imageItem.getViewBox()
try:
if viewBox.sceneBoundingRect().contains(pos):
mousePoint = viewBox.mapSceneToView(pos)
x, y = map(int, (mousePoint.x(), mousePoint.y()))
if (0 <= x < self.imageItem.image.shape[0]) & (0 <= y < self.imageItem.image.shape[1]): # within bounds
self.coordsLabel.setText(u"<div style='font-size: 12pt;background-color:#111111;'>x={0},"
u" <span style=''>y={1}</span>, <span style=''>I={2}</span>"\
.format(x, y, self.imageItem.image[x, y]))
else:
self.coordsLabel.setText(u"<div style='font-size: 12pt;background-color:#111111;'>x= ,"
u" <span style=''>y= </span>, <span style=''>I= </span>")
except AttributeError:
pass
class StackViewer(ImageView):
"""
PG ImageView subclass to view projections or sinograms of a tomography dataset
"""
def __init__(self, data=None, view_label=None, *args, **kwargs):
super(StackViewer, self).__init__(*args, **kwargs)
# self.getImageItem().setAutoDownsample(True)
self.view_label = QtGui.QLabel(self)
self.view_label.setText('No: ')
self.view_spinBox = QtGui.QSpinBox(self)
self.view_spinBox.setKeyboardTracking(False)
if data is not None:
self.setData(data)
l = QtGui.QHBoxLayout()
l.setContentsMargins(0, 0, 0, 0)
l.addWidget(self.view_label)
l.addWidget(self.view_spinBox)
l.addStretch(1)
w = QtGui.QWidget()
w.setLayout(l)
self.ui.gridLayout.addWidget(self.view_label, 1, 1, 1, 1)
self.ui.gridLayout.addWidget(self.view_spinBox, 1, 2, 1, 1)
self.ui.menuBtn.setParent(None)
self.ui.roiBtn.setParent(None)
self.sigTimeChanged.connect(self.indexChanged)
self.view_spinBox.valueChanged.connect(self.setCurrentIndex)
def setData(self, data):
self.data = data
self.setImage(self.data)
self.autoLevels()
self.view_spinBox.setRange(0, self.data.shape[0] - 1)
self.getImageItem().setRect(QtCore.QRect(0, 0, self.data.rawdata.shape[0], self.data.rawdata.shape[1]))
def indexChanged(self, ind, time):
self.view_spinBox.setValue(ind)
def setIndex(self, ind):
self.setCurrentIndex(ind)
self.view_spinBox.setValue(ind)
@property
def currentdata(self):
return self.data[self.data.currentframe].transpose() # Maybe we need to transpose this
def resetImage(self):
self.setImage(self.data, autoRange=False)
self.setIndex(self.currentIndex)
class ROImageOverlay(pg.ROI):
sigTranslated = QtCore.Signal(int, int)
def __init__(self, data, bg_imageItem, pos, constrainX=False, constrainY=True, translateSnap=True, **kwargs):
size = bg_imageItem.image.shape
super(ROImageOverlay, self).__init__(pos, translateSnap=translateSnap, size=size, pen=pg.mkPen(None), **kwargs)
self.data = data
self.bg_imgeItem = bg_imageItem
self._y_constrained = constrainY
self._x_constrained = constrainX
self._image_overlap = np.empty(size, dtype='float32')
self._mask = np.zeros(size, dtype=bool)
self.currentImage = None
self.currentIndex = None
self.flipped = False
self.setCurrentImage(-1)
self.flipCurrentImage()
self.imageItem = pg.ImageItem(self.currentImage)
self.imageItem.setParentItem(self)
self.updateImage()
def setCurrentImage(self, idx):
self.currentImage = np.array(self.data[idx]).astype('float32')
self.currentIndex = idx
if self.flipped:
self.flipCurrentImage(toggle=False)
def constrainX(self, val):
self._x_constrained = val
def constrainY(self, val):
self._y_constrained = val
def flipCurrentImage(self, toggle=True):
self.currentImage = np.flipud(self.currentImage)
if toggle:
self.flipped = not self.flipped
@property
def image_overlap(self):
self._image_overlap.fill(0)
x, y = self.pos()
if x == 0:
x_slc, bg_x_slc = None, None
elif x < 0:
x_slc, bg_x_slc = slice(-x, None), slice(None, x)
elif x > 0:
x_slc, bg_x_slc = slice(None, -x), slice(x, None)
if y == 0:
y_slc, bg_y_slc = None, None
elif y < 0:
y_slc, bg_y_slc = slice(-y, None), slice(None, y)
elif y > 0:
y_slc, bg_y_slc = slice(None, -y), slice(y, None)
slc, bg_slc = (x_slc, y_slc), (bg_x_slc, bg_y_slc)
self._image_overlap[slc] = self.bg_imgeItem.image[bg_slc]
return self._image_overlap
def updateImage(self, autolevels=None):
self.imageItem.setImage(self.currentImage - self.image_overlap, autoLevels=autolevels)
def translate(self, *args, **kwargs):
super(ROImageOverlay, self).translate(*args, **kwargs)
self.updateImage()
self.sigTranslated.emit(*self.pos())
def resetImage(self):
self.setCurrentImage(self.currentIndex)
self.updateImage()
def mouseDragEvent(self, ev):
"""
Overload ROI.mouseDragEvent to set all vertical offsets to zero and constrain dragging to horizontal axis
"""
if ev.isStart():
if ev.button() == QtCore.Qt.LeftButton:
self.setSelected(True)
if self.translatable:
self.isMoving = True
self.preMoveState = self.getState()
self.cursorOffset = self.pos() - self.mapToParent(ev.buttonDownPos())
self.sigRegionChangeStarted.emit(self)
ev.accept()
else:
ev.ignore()
elif ev.isFinish():
if self.translatable:
if self.isMoving:
self.stateChangeFinished()
self.isMoving = False
return
if self.translatable and self.isMoving and ev.buttons() == QtCore.Qt.LeftButton:
snap = True if (ev.modifiers() & QtCore.Qt.ControlModifier) else None
newPos = self.mapToParent(ev.pos()) + self.cursorOffset
if self._y_constrained:
newPos.y = self.pos().y
if self._x_constrained:
newPos.x = self.pos().x
self.translate(newPos - self.pos(), snap=snap, finish=False)
def keyPressEvent(self, ev):
if ev.key() == QtCore.Qt.Key_Right:
self.translate(pg.Point((1, 0)))
elif ev.key() == QtCore.Qt.Key_Left:
self.translate(pg.Point((-1, 0)))
elif ev.key() == QtCore.Qt.Key_Up:
self.translate(pg.Point((0, 1)))
elif ev.key() == QtCore.Qt.Key_Down:
self.translate(pg.Point((0, -1)))
ev.accept()
class ProjectionViewer(QtGui.QWidget):
"""
Class that holds a stack viewer, an ROImageOverlay and a few widgets to allow manual center detection
"""
sigCenterChanged = QtCore.Signal(float)
def __init__(self, data, view_label=None, center=None, *args, **kwargs):
super(ProjectionViewer, self).__init__(*args, **kwargs)
self.stackViewer = StackViewer(data, view_label=view_label)
self.imageItem = self.stackViewer.imageItem
self.data = self.stackViewer.data
self.normalized = False
self.flat = np.median(self.data.flats, axis=0).transpose()
self.dark = np.median(self.data.darks, axis=0).transpose()
self.roi = ROImageOverlay(self.data, self.imageItem, [0, 0])
# self.stackViewer.getHistogramWidget().setImageItem(self.roi.imageItem)
self.imageItem.sigImageChanged.connect(self.roi.updateImage)
self.stackViewer.view.addItem(self.roi)
self.roi_histogram = pg.HistogramLUTWidget(image=self.roi.imageItem, parent=self)
self.stackViewer.ui.gridLayout.addWidget(self.roi_histogram, 0, 3, 1, 2)
self.stackViewer.keyPressEvent = self.keyPressEvent
self.cor_widget = QtGui.QWidget(self)
clabel = QtGui.QLabel('Rotation Center:')
clabel.setAlignment(QtCore.Qt.AlignRight)
olabel = QtGui.QLabel('Offset:')
self.centerBox = QtGui.QDoubleSpinBox(parent=self.cor_widget) #QtGui.QLabel(parent=self.cor_widget)
self.centerBox.setDecimals(1)
self.setCenterButton = QtGui.QPushButton('Set in Pipeline')
originBox = QtGui.QLabel(parent=self.cor_widget)
originBox.setText('x={} y={}'.format(0, 0))
center = center if center is not None else data.shape[1]/2.0
self.centerBox.setValue(center) #setText(str(center))
h1 = QtGui.QHBoxLayout()
h1.setAlignment(QtCore.Qt.AlignLeft)
h1.setContentsMargins(0, 0, 0, 0)
h1.addWidget(clabel)
h1.addWidget(self.centerBox)
h1.addWidget(self.setCenterButton)
h1.addWidget(olabel)
h1.addWidget(originBox)
plabel = QtGui.QLabel('Overlay Projection No:')
plabel.setAlignment(QtCore.Qt.AlignRight)
spinBox = QtGui.QSpinBox(parent=self.cor_widget)
#TODO data shape seems to be on larger than the return from slicing it with [:-1]
spinBox.setRange(0, data.shape[0])
slider = QtGui.QSlider(orientation=QtCore.Qt.Horizontal, parent=self.cor_widget)
slider.setRange(0, data.shape[0])
spinBox.setValue(data.shape[0])
slider.setValue(data.shape[0])
flipCheckBox = QtGui.QCheckBox('Flip Overlay', parent=self.cor_widget)
flipCheckBox.setChecked(True)
constrainYCheckBox = QtGui.QCheckBox('Constrain Y', parent=self.cor_widget)
constrainYCheckBox.setChecked(True)
constrainXCheckBox = QtGui.QCheckBox('Constrain X', parent=self.cor_widget)
constrainXCheckBox.setChecked(False)
# rotateCheckBox = QtGui.QCheckBox('Enable Rotation', parent=self.cor_widget)
# rotateCheckBox.setChecked(False)
self.normCheckBox = QtGui.QCheckBox('Normalize', parent=self.cor_widget)
h2 = QtGui.QHBoxLayout()
h2.setAlignment(QtCore.Qt.AlignLeft)
h2.setContentsMargins(0, 0, 0, 0)
h2.addWidget(plabel)
h2.addWidget(spinBox)
h2.addWidget(flipCheckBox)
h2.addWidget(constrainXCheckBox)
h2.addWidget(constrainYCheckBox)
# h2.addWidget(rotateCheckBox) # This needs to be implemented correctly
h2.addWidget(self.normCheckBox)
h2.addStretch(1)
spinBox.setFixedWidth(spinBox.width())
v = QtGui.QVBoxLayout(self.cor_widget)
v.addLayout(h1)
v.addLayout(h2)
v.addWidget(slider)
l = QtGui.QGridLayout(self) # VBoxLayout(self)
l.setContentsMargins(0, 0, 0, 0)
l.addWidget(self.cor_widget)
l.addWidget(self.stackViewer)
slider.valueChanged.connect(spinBox.setValue)
slider.valueChanged.connect(self.stackViewer.resetImage)
spinBox.valueChanged.connect(self.changeOverlayProj)
flipCheckBox.stateChanged.connect(self.flipOverlayProj)
constrainYCheckBox.stateChanged.connect(lambda v: self.roi.constrainY(v))
constrainXCheckBox.stateChanged.connect(lambda v: self.roi.constrainX(v))
# rotateCheckBox.stateChanged.connect(self.addRotateHandle)
self.normCheckBox.stateChanged.connect(self.normalize)
self.stackViewer.sigTimeChanged.connect(lambda: self.normalize(False))
self.roi.sigTranslated.connect(self.setCenter)
self.roi.sigTranslated.connect(lambda x, y: originBox.setText('x={} y={}'.format(x, y)))
self.hideCenterDetection()
def changeOverlayProj(self, idx):
self.normCheckBox.setChecked(False)
self.roi.setCurrentImage(idx)
self.roi.updateImage()
def setCenter(self, x, y):
center = (self.data.shape[1] + x)/2.0
self.centerBox.setValue(center) # setText(str(center))
self.sigCenterChanged.emit(center)
def hideCenterDetection(self):
self.normalize(False)
self.cor_widget.hide()
self.roi_histogram.hide()
self.roi.setVisible(False)
def showCenterDetection(self):
self.cor_widget.show()
self.roi_histogram.show()
self.roi.setVisible(True)
def updateROIFromCenter(self, center):
s = self.roi.pos()[0]
self.roi.translate(pg.Point((2 * center - self.data.shape[1] - s, 0)))
def flipOverlayProj(self, val):
self.roi.flipCurrentImage()
self.roi.updateImage()
def addRotateHandle(self, val):
if val:
self.addRotateHandle.handle = self.roi.addRotateHandle([0,1], [0.2, 0.2])
else:
self.roi.removeHandle(self.addRotateHandle.handle)
def normalize(self, val):
if val and not self.normalized:
proj = (self.imageItem.image - self.dark)/(self.flat - self.dark)
overlay = self.roi.currentImage
if self.roi.flipped:
overlay = np.flipud(overlay)
overlay = (overlay - self.dark)/(self.flat - self.dark)
if self.roi.flipped:
overlay = np.flipud(overlay)
self.roi.currentImage = overlay
self.roi.updateImage(autolevels=True)
self.stackViewer.setImage(proj, autoRange=False, autoLevels=True)
self.stackViewer.updateImage()
self.normalized = True
elif not val and self.normalized:
self.stackViewer.resetImage()
self.roi.resetImage()
self.normalized = False
self.normCheckBox.setChecked(False)
def keyPressEvent(self, ev):
super(ProjectionViewer, self).keyPressEvent(ev)
if self.roi.isVisible():
self.roi.keyPressEvent(ev)
else:
super(StackViewer, self.stackViewer).keyPressEvent(ev)
ev.accept()
class PreviewViewer(QtGui.QSplitter):
"""
Viewer class to show reconstruction previews in a PG ImageView, along with the function pipeline settings for the
corresponding preview
"""
def __init__(self, dim, maxpreviews=None, *args, **kwargs):
super(PreviewViewer, self).__init__(*args, **kwargs)
self.maxpreviews = maxpreviews if maxpreviews is not None else 10
self.dim = dim
self.previews = ArrayDeque(arrayshape=(dim, dim), maxlen=self.maxpreviews)
self.datatrees = deque(maxlen=self.maxpreviews)
self.data = deque(maxlen=self.maxpreviews)
self.setOrientation(QtCore.Qt.Horizontal)
l = QtGui.QVBoxLayout()
l.setContentsMargins(0, 0, 0, 0)
self.functionform = QtGui.QStackedWidget()
self.setPipelineButton = QtGui.QPushButton(self)
self.setPipelineButton.setText("Set As Pipeline")
l.addWidget(self.functionform)
l.addWidget(self.setPipelineButton)
panel = QtGui.QWidget(self)
panel.setLayout(l)
self.imageview = ImageView(self)
self.imageview.ui.roiBtn.setParent(None)
self.imageview.ui.roiBtn.setParent(None)
self.deleteButton = QtGui.QPushButton(self.imageview)
self.deleteButton.setText("")
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap("gui/icons_40.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.deleteButton.setIcon(icon)
self.imageview.ui.gridLayout.addWidget(self.deleteButton, 1, 1, 1, 1)
self.setCurrentIndex = self.imageview.setCurrentIndex
self.addWidget(panel)
self.addWidget(self.imageview)
self.imageview.sigDeletePressed.connect(self.removePreview)
self.setPipelineButton.clicked.connect(self.defaultsButtonClicked)
self.deleteButton.clicked.connect(self.removePreview)
self.imageview.sigTimeChanged.connect(self.indexChanged)
@ QtCore.Slot(object, object)
def indexChanged(self, index, time):
try:
self.functionform.setCurrentWidget(self.datatrees[index])
except IndexError as e:
print 'index {} does not exist'.format(index)
# Could be leaking memory if I don't explicitly delete the datatrees that are being removed
# from the previewdata deque but are still in the functionform widget? Hopefully python gc is taking good care of me
def addPreview(self, image, funcdata):
self.previews.appendleft(np.flipud(image))
functree = DataTreeWidget()
functree.setHeaderHidden(True)
functree.setData(funcdata, hideRoot=True)
self.data.appendleft(funcdata)
self.datatrees.appendleft(functree)
self.functionform.addWidget(functree)
self.imageview.setImage(self.previews)
self.functionform.setCurrentWidget(functree)
def removePreview(self):
if len(self.previews) > 0:
idx = self.imageview.currentIndex
self.functionform.removeWidget(self.datatrees[idx])
del self.previews[idx]
del self.datatrees[idx]
del self.data[idx]
if len(self.previews) == 0:
self.imageview.clear()
else:
self.imageview.setImage(self.previews)
def defaultsButtonClicked(self):
current_data = self.data[self.imageview.currentIndex]
print 'Default data ', current_data
fmanager.set_function_pipeline(current_data)
class ReconstructionViewer(QtGui.QWidget):
def __init__(self, parent=None):
super(ReconstructionViewer, self).__init__(parent=parent)
self.stack_viewer = StackViewer()
self.path_edit = QtGui.QLineEdit(parent=self)
self.path_edit.setReadOnly(True)
self.browse_button = QtGui.QPushButton(parent=self)
self.browse_button.setText('Select Reconstruction')
layout = QtGui.QGridLayout(self)
layout.addWidget(self.path_edit, 0, 0, 1, 1)
layout.addWidget(self.browse_button, 0, 1, 1, 1)
layout.addWidget(self.stack_viewer, 1, 0, 2, 2)
self.browse_button.clicked.connect(self.openDataset)
def openDataset(self, path=None):
if path is None:
path = QtGui.QFileDialog.getOpenFileNames(self, 'Open Reconstruction Data', os.path.expanduser('~'))[0]
if path:
data = loader.StackImage(path)
self.stack_viewer.setData(data)
if isinstance(path, list):
path = os.path.split(path[0])[0]
self.path_edit.setText(path)
"""
Example volume rendering
Controls:
* 1 - toggle camera between first person (fly), regular 3D (turntable) and
arcball
* 2 - toggle between volume rendering methods
* 3 - toggle between stent-CT / brain-MRI image
* 4 - toggle between colormaps
* 0 - reset cameras
* [] - decrease/increase isosurface threshold
With fly camera:
* WASD or arrow keys - move around
* SPACE - brake
* FC - move up-down
* IJKL or mouse - look around
"""
class VolumeViewer(QtGui.QWidget):
sigImageChanged=QtCore.Signal()
def __init__(self,path=None,data=None,*args,**kwargs):
super(VolumeViewer, self).__init__()
self.levels=[0,1]
l = QtGui.QHBoxLayout()
l.setContentsMargins(0,0,0,0)
l.setSpacing(0)
self.volumeRenderWidget=VolumeRenderWidget()
l.addWidget(self.volumeRenderWidget.native)
self.HistogramLUTWidget = pg.HistogramLUTWidget(image=self, parent=self)
self.HistogramLUTWidget.setMaximumWidth(self.HistogramLUTWidget.minimumWidth()+15)# Keep static width
self.HistogramLUTWidget.setMinimumWidth(self.HistogramLUTWidget.minimumWidth()+15)
l.addWidget(self.HistogramLUTWidget)
self.xregion = SliceWidget(parent=self)
self.yregion = SliceWidget(parent=self)
self.zregion = SliceWidget(parent=self)
self.xregion.item.region.setRegion([0,5000])
self.yregion.item.region.setRegion([0,5000])
self.zregion.item.region.setRegion([0,5000])
self.xregion.sigSliceChanged.connect(self.setVolume) #change to setVolume
self.yregion.sigSliceChanged.connect(self.setVolume)
self.zregion.sigSliceChanged.connect(self.setVolume)
l.addWidget(self.xregion)
l.addWidget(self.yregion)
l.addWidget(self.zregion)
self.setLayout(l)
# self.setVolume(vol=data,path=path)
# self.volumeRenderWidget.export('video.mp4',fps=25,duration=10.)
# self.writevideo()
def getSlice(self):
xslice=self.xregion.getSlice()
yslice=self.yregion.getSlice()
zslice=self.zregion.getSlice()
return xslice,yslice,zslice
def setVolume(self,vol=None,path=None):
sliceobj=self.getSlice()
self.volumeRenderWidget.setVolume(vol,path,sliceobj)
self.volumeRenderWidget.update()
if vol is not None or path is not None:
self.sigImageChanged.emit()
self.xregion.item.region.setRegion([0,self.volumeRenderWidget.vol.shape[0]])
self.yregion.item.region.setRegion([0,self.volumeRenderWidget.vol.shape[1]])
self.zregion.item.region.setRegion([0,self.volumeRenderWidget.vol.shape[2]])
def setLevels(self, levels, update=True):
print 'levels:',levels
self.levels=levels
self.setLookupTable()
def setLookupTable(self, lut=None, update=True):
try:
table=self.HistogramLUTWidget.item.gradient.colorMap().color/256.
pos=self.HistogramLUTWidget.item.gradient.colorMap().pos
#table=np.clip(table*(self.levels[1]-self.levels[0])+self.levels[0],0.,1.)
table[:,3]=pos
table=np.vstack([np.array([[0,0,0,0]]),table,np.array([[1,1,1,1]])])
pos=np.hstack([[0],pos*(self.levels[1]-self.levels[0])+self.levels[0],[1]])
self.volumeRenderWidget.volume.cmap = Colormap(table,controls=pos)
except AttributeError as ex:
print ex
def getHistogram(self, bins='auto', step='auto', targetImageSize=100, targetHistogramSize=500, **kwds):
"""Returns x and y arrays containing the histogram values for the current image.
For an explanation of the return format, see numpy.histogram().
The *step* argument causes pixels to be skipped when computing the histogram to save time.
If *step* is 'auto', then a step is chosen such that the analyzed data has
dimensions roughly *targetImageSize* for each axis.
The *bins* argument and any extra keyword arguments are passed to
np.histogram(). If *bins* is 'auto', then a bin number is automatically
chosen based on the image characteristics:
* Integer images will have approximately *targetHistogramSize* bins,
with each bin having an integer width.
* All other types will have *targetHistogramSize* bins.
This method is also used when automatically computing levels.
"""
if self.vol is None:
return None,None
if step == 'auto':
step = (np.ceil(self.vol.shape[0] / targetImageSize),
np.ceil(self.vol.shape[1] / targetImageSize))
if np.isscalar(step):
step = (step, step)
stepData = self.vol[::step[0], ::step[1]]
if bins == 'auto':
if stepData.dtype.kind in "ui":
mn = stepData.min()
mx = stepData.max()
step = np.ceil((mx-mn) / 500.)
bins = np.arange(mn, mx+1.01*step, step, dtype=np.int)
if len(bins) == 0:
bins = [mn, mx]
else:
bins = 500
kwds['bins'] = bins
print kwds
hist = np.histogram(stepData, **kwds)
return hist[1][:-1], hist[0]
@property
def vol(self):
return self.volumeRenderWidget.vol
#
# @volumeRenderWidget.connect
# def on_frame(self,event):
# self.volumeRenderWidget.cam1.auto_roll
def writevideo(self,fps=25):
writer = imageio.save('foo.mp4', fps=25)
self.volumeRenderWidget.events.draw.connect(lambda e: writer.append_data(self.render()))
self.volumeRenderWidget.events.close.connect(lambda e: writer.close())
class VolumeRenderWidget(scene.SceneCanvas):
def __init__(self,vol=None, path=None, size=(800,600), show=False):
super(VolumeRenderWidget, self).__init__(keys='interactive', size=size, show=show)
# Prepare canvas
self.measure_fps()
#self.unfreeze()
# Set up a viewbox to display the image with interactive pan/zoom
self.view = self.central_widget.add_view()
self.vol=None
self.setVolume(vol,path)
self.volume=None
# Create three cameras (Fly, Turntable and Arcball)
fov = 60.
self.cam1 = scene.cameras.FlyCamera(parent=self.view.scene, fov=fov, name='Fly')
self.cam2 = scene.cameras.TurntableCamera(parent=self.view.scene, fov=fov, name='Turntable')
self.cam3 = scene.cameras.ArcballCamera(parent=self.view.scene, fov=fov, name='Arcball')
self.view.camera = self.cam2 # Select turntable at first
def setVolume(self, vol=None, path=None, sliceobj=None):
print 'slice:',sliceobj
if vol is None:
vol=self.vol
if path is not None:
if '*' in path:
vol=loader.loadimageseries(path)
elif os.path.splitext(path)[-1]=='.npy':
vol=loader.loadimage(path)
else:
vol=loader.loadtiffstack(path)
if vol is None:
return
self.vol = vol
if slice is not None:
print 'preslice:',vol.shape
slicevol=self.vol[sliceobj]
print 'postslice:',vol.shape
else:
slicevol=self.vol
# Set whether we are emulating a 3D texture
emulate_texture = False
# Create the volume visuals
if self.volume is None:
self.volume = scene.visuals.Volume(slicevol, parent=self.view.scene,emulate_texture=emulate_texture)
self.volume.method='translucent'
else:
self.volume.set_data(slicevol)
self.volume._create_vertex_data() #TODO: Try using this instead of slicing array?
# Translate the volume into the center of the view (axes are in strange order for unkown )
self.volume.transform = scene.STTransform(translate=(-vol.shape[2]/2,-vol.shape[1]/2,-vol.shape[0]/2))
# Implement key presses
def on_key_press(self, event):
if event.text == '1':
cam_toggle = {self.cam1: self.cam2, self.cam2: self.cam3, self.cam3: self.cam1}
self.view.camera = cam_toggle.get(self.view.camera, self.cam2)
print(self.view.camera.name + ' camera')
elif event.text == '2':
pass
elif event.text == '3':
pass
elif event.text == '4':
pass
elif event.text == '0':
self.cam1.set_range()
self.cam3.set_range()
elif event.text != '' and event.text in '[]':
s = -0.025 if event.text == '[' else 0.025
self.volume.threshold += s
th = self.volume.threshold
print("Isosurface threshold: %0.3f" % th)
class SliceWidget(pg.HistogramLUTWidget):
sigSliceChanged = QtCore.Signal()
def __init__(self, *args, **kwargs):
super(SliceWidget, self).__init__(*args, **kwargs)
self.item.paint = lambda *x: None
self.item.vb.deleteLater()
self.item.gradient.gradRect.hide()
self.item.gradient.allowAdd = False
self.setMinimumWidth(70)
self.setMaximumWidth(70)
self.item.sigLookupTableChanged.connect(self.ticksChanged)
self.setSizePolicy(QtGui.QSizePolicy.Minimum,QtGui.QSizePolicy.Expanding)
def sizeHint(self):
return QtCore.QSize(70, 200)
def ticksChanged(self,LUT):
self.sigSliceChanged.emit()
#tuple(sorted(LUT.gradient.ticks.values()))
def getSlice(self):
bounds=sorted(self.item.gradient.ticks.values())
bounds=(bounds[0]*self.item.region.getRegion()[1],bounds[1]*self.item.region.getRegion()[1])
return slice(*bounds)
class VolumeVisual(scene.visuals.Volume):
def set_data(self, vol, clim=None):
""" Set the volume data.
Parameters
----------
vol : ndarray
The 3D volume.
clim : tuple | None
Colormap limits to use. None will use the min and max values.
"""
# Check volume
if not isinstance(vol, np.ndarray):
raise ValueError('Volume visual needs a numpy array.')
if not ((vol.ndim == 3) or (vol.ndim == 4 and vol.shape[-1] <= 4)):
raise ValueError('Volume visual needs a 3D image.')
# Handle clim
if clim is not None:
clim = np.array(clim, float)
if not (clim.ndim == 1 and clim.size == 2):
raise ValueError('clim must be a 2-element array-like')
self._clim = tuple(clim)
self._clim = vol.min(), vol.max() #NOTE: THIS IS MODIFIED BY RP TO RESET MIN/MAX EACH TIME
# Apply clim
vol = np.array(vol, dtype='float32', copy=False)