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How to use leftMouseDragged method in pyatom
Best Python code snippet using pyatom_python
SeriesGraphicsView.py
Source:SeriesGraphicsView.py 
1from pyqtgraph import ImageView as PGImageView2import numpy as np3import math4from PyQt5.QtCore import Qt5from PyQt5 import QtCore6from PyQt5.QtCore import pyqtSignal7import pyqtgraph as pg8from pyqtgraph.GraphicsScene import mouseEvents9from PyQt5.QtWidgets import QFrame, QHBoxLayout10from itertools import groupby11from scripts.UI.Graphics.OverlayGraphics import OverlayGraphics12from scripts.UI.Stats.ImageStats import ImageStats13from scripts.ToolBox.AutoSegmentation import AutoSegmentation14from scripts.UI.Cursor import Cursor15from scripts.Helper.SegmentationRegion import SegmentationRegion16"""17Widget that takes a viewbox and image item to display images associated with Series18"""19class SeriesGraphicsView(PGImageView):20 newSegmentationBundle = pyqtSignal(object)21 def __init__(self, parent, toolBar):22 super().__init__(parent=parent, view=ViewBox(), imageItem=ImageItem(toolBar))23 self.toolBar = toolBar24 self.toolBar.playBtn.clicked.connect(lambda x: self.play(5))25 self.toolBar.colorMapBtn.colorMapSelected.connect(self.setLookupTable)26 self.toolBar.overlayBtn.overlaySelected.connect(self.setOverlayCursor)27 self.cursor = Cursor()28 self.overlay = OverlayGraphics(self.view, self.imageItem, self.toolBar)29 self.autoSeg = AutoSegmentation(self, self.toolBar)30 self.imageStats = ImageStats(self)31 self.initUI()32 def initUI(self):33 self.centralFrame = QFrame(self)34 self.centralFrame.setFrameShape(QFrame.NoFrame)35 self.centralFrame.setFrameShadow(QFrame.Raised)36 self.centralFrame.setContentsMargins(0, 0, 0, 0)37 self.centralFrame.setStyleSheet("border: none;")38 self.setMinimumWidth(500)39 self.setMinimumHeight(300)40 self.setObjectName("imageView")41 self.ui.histogram.hide()42 self.ui.roiBtn.hide()43 self.ui.menuBtn.hide()44 self.ui.roiPlot.setVisible(False)45 self.ignorePlay = False46 self.ui.splitter.setSizes([self.height() - 35, 35])47 self.splitterHandle = self.ui.splitter.handle(1)48 self.splitterHandle.setEnabled(False)49 self.centralLayout = QHBoxLayout(self.centralFrame)50 self.centralLayout.addWidget(self.centralFrame)51 self.centralLayout.setContentsMargins(0, 0, 0, 0)52 self.setLayout(self.centralLayout)53 """54 Called when new patient is loaded. Calls reset function55 ================== ===========================================================================56 **Arguments:**57 patient loaded patient58 ================== ===========================================================================59 """60 def newPatient(self, patient):61 self.reset()62 """63 Clears image item and sets image to None64 """65 def reset(self):66 self.clear()67 self.view.setCursor(self.cursor.DefaultCursor)68 # self.imageStats.disable()69 self.imageItem.lut = self.toolBar.colorMapBtn.colorMap70 """71 Sets cursor for series viewbox72 ================== ===========================================================================73 **Arguments:**74 activeOverlay the overlay selected in the toolbar75 ================== ===========================================================================76 """77 def setOverlayCursor(self, overlayColor):78 if overlayColor is None:79 self.view.setCursor(self.cursor.DefaultCursor)80 else:81 self.view.setCursor(self.cursor.CrossCursor)82 """83 Sets color map for series images84 ================== ===========================================================================85 **Arguments:**86 lut lookup table87 ================== ===========================================================================88 """89 def setLookupTable(self, lut):90 self.imageItem.setLookupTable(lut)91 """92 Iterates through the image slices at specified rate93 ================== ===========================================================================94 **Arguments:**95 rate play rate96 ================== ===========================================================================97 """98 def play(self, rate):99 if self.ignorePlay:100 return101 if self.playTimer.isActive():102 self.playTimer.stop()103 self.toolBar.playBtn.setPlayState()104 return105 if self.currentIndex == (self.image.shape[0] - 1):106 self.setCurrentIndex(0)107 self.toolBar.playBtn.setPauseState()108 super().play(rate)109 """110 Checks for completion of play111 """112 def timeout(self):113 if self.currentIndex == (self.image.shape[0] - 1):114 self.playTimer.stop()115 self.toolBar.playBtn.setPlayState()116 return117 super().timeout()118 """119 Displays the images associated with the active series.120 ================== ===========================================================================121 **Arguments:**122 series the series object123 ================== ===========================================================================124 """125 def seriesSelected(self, series):126 self.reset()127 if series is None:128 return129 images = []130 for image in series.images:131 images.append(image.pixel_array)132 imageData = np.array(images)133 # pytgraph assumes images are in column-major order (col, row) so we need to transpose data into that format134 imageData = imageData.transpose((0, 2, 1))135 # scaling the image to fit the viewbox dimensions is causing all sorts of issues. set to 1 for now136 imageScale = 1137 # imageScale = self.getImageScale(imageData)138 # set image for imageView139 self.setImage(imageData, scale=(imageScale, imageScale))140 self.setViewScale(imageScale) # adjust view to fit new image141 self.view.addItem(self.imageItem)142 # show image stats panel143 # self.imageStats.enable()144 self.toolBar.colorMapBtn.colorMap = self.imageItem.lut145 """146 Updates the imageROI to match the image region specified by the mask. Mask is assumed to be147 in mask item coordinates.148 ================== ===========================================================================149 **Arguments:**150 mask the mask151 ================== ===========================================================================152 """153 def newMask(self, mask):154 self.segmentationBundle = SegmentationBundle()155 regions = mask.regions156 regionsSorted = sorted(regions, key=lambda x: x.id)157 regionsGroupedBy = groupby(regionsSorted, key=lambda x: x.id)158 regionsGrouped = {}159 for _id, _regions in regionsGroupedBy:160 regionsGrouped[_id] = list(_regions)161 for _id, _regions in regionsGrouped.items():162 mask = sum(region.mask for region in _regions)163 mask[mask > 1] = 0164 maskCoordinates = np.argwhere(mask)165 maskCoordinates = [QtCore.QPointF(coordinate[0], coordinate[1]) for coordinate in maskCoordinates]166 maskCoordinates = [[math.floor(coordinate.x()), math.floor(coordinate.y())] for coordinate in167 maskCoordinates]168 mask = np.zeros((self.image.shape[1], self.image.shape[2]))169 x_coords = [c[0] for c in maskCoordinates]170 y_coords = [c[1] for c in maskCoordinates]171 mask[x_coords, y_coords] = 1172 mask[mask == 0] = np.nan # convert mask zeros to nan to differentiate between image zeros173 mask = np.ma.masked_invalid(mask) # create a mask array to handle nan during multiplication174 masked_image = mask * self.image # multiply masked array by image175 masked_image = masked_image.filled(176 np.nan) # convert back to numpy array, filling in masked values with nan177 masked_image = masked_image.transpose((0, 2, 1)) # transpose image back to row-major order (row, col)178 region = SegmentationRegion()179 region.image = masked_image180 region.id = _id181 self.segmentationBundle.regions.append(region)182 self.newSegmentationBundle.emit(self.segmentationBundle)183 """184 Changes the overlaid text based on the current image185 """186 def timeLineChanged(self):187 super().timeLineChanged()188 """189 Adjusts the view limits based on the image to display. Prevents zooming out too far.190 Centers image within the view.191 ================== ===========================================================================192 **Arguments:**193 imageScale the scale of the image194 ================== ===========================================================================195 """196 def setViewScale(self, imageScale):197 self.view.setLimits(xMin=0,198 xMax=self.imageItem.width() * imageScale,199 yMin=0,200 yMax=self.imageItem.height() * imageScale,201 minXRange=1,202 minYRange=1)203 # viewWidth = self.view.screenGeometry().width()204 # viewHeight = self.view.screenGeometry().height()205 # if viewWidth > viewHeight:206 # self.view.setLimits(xMin=-(viewWidth - self.imageItem.width() * imageScale),207 # xMax=viewWidth,208 # yMin=0,209 # yMax=viewHeight,210 # minXRange=1,211 # minYRange=1)212 #213 # else:214 # self.view.setLimits(xMin=0,215 # xMax=viewWidth,216 # yMin=-(viewHeight - self.imageItem.height() * imageScale),217 # yMax=viewHeight,218 # minXRange=1,219 # minYRange=1)220 self.view.translateBy(x=0, y=0)221 aspectRatio = self.image.shape[1] / self.image.shape[2] # width / height ratio222 self.view.setAspectLocked(lock=True, ratio=aspectRatio)223 """224 Determines the proper image scale based on the viewbox.225 ================== ===========================================================================226 **Arguments:**227 imageData the ndarray associated with the image228 229 **Returns:**230 imageScale the image scale231 ================== ===========================================================================232 """233 def getImageScale(self, imageData):234 viewWidth = self.view.screenGeometry().width()235 viewHeight = self.view.screenGeometry().height()236 if viewWidth < viewHeight:237 imageScale = viewWidth / imageData.shape[1]238 else:239 imageScale = viewHeight / imageData.shape[2]240 return imageScale241class SegmentationBundle:242 def __init__(self):243 self.regions = []244"""245The pyqtgraph viewbox. The viewbox displays items.246"""247class ViewBox(pg.ViewBox):248 def __init__(self):249 super().__init__()250 self.cursor = Cursor()251 self.initUI()252 def initUI(self):253 self.setAspectLocked(True)254 self.setMouseMode(pg.ViewBox.PanMode)255 def mouseDragEvent(self, ev, axis=None):256 if ev.isStart():257 self.setCursor(self.cursor.ClosedHandCursor)258 if ev.isFinish():259 self.setCursor(self.cursor.DefaultCursor)260 super().mouseDragEvent(ev, axis)261 def mouseClickEvent(self, ev):262 if ev.button() == Qt.LeftButton:263 super().mouseClickEvent(ev)264 else:265 return266 def wheelEvent(self, ev, axis=None):267 super().wheelEvent(ev, axis)268 def resizeEvent(self, ev):269 super().resizeEvent(ev)270"""271The pyqtgraph image item. An image item stores the images.272"""273class ImageItem(pg.ImageItem):274 leftMouseDragged = pyqtSignal(mouseEvents.MouseDragEvent)275 mouseHovered = pyqtSignal(mouseEvents.HoverEvent)276 contextMenuTriggered = pyqtSignal(object)277 def __init__(self, toolBar):278 super().__init__()279 self.toolBar = toolBar280 def mouseDragEvent(self, ev, axis=None):281 if self.toolBar.overlayBtn.overlayColor is None:282 super().mouseDragEvent(ev)283 return284 if ev.button() == Qt.LeftButton:285 self.leftMouseDragged.emit(ev)286 def hoverEvent(self, ev):287 if self.toolBar.overlayBtn.overlayColor is None:288 super().hoverEvent(ev)289 self.mouseHovered.emit(ev)290 return291 self.mouseHovered.emit(ev)292 ev.acceptDrags(QtCore.Qt.LeftButton)293 def contextMenuEvent(self, event):...
MaskGraphicsView.py
Source:MaskGraphicsView.py
1from PyQt5.QtCore import pyqtSignal, Qt2import pyqtgraph as pg3from pyqtgraph import GraphicsView as PGGraphicsView4from pyqtgraph.GraphicsScene import mouseEvents5import numpy as np6from PIL import Image, ImageDraw7from PyQt5.QtWidgets import QFrame, QHBoxLayout8from scripts.UI.Graphics.KernelGraphics import KernelGraphics9from scripts.UI.Cursor import Cursor10from scripts.Helper.SegmentationRegion import SegmentationRegion11"""12Widget displays mask associated with overlay drawn on series graphics13"""14class MaskGraphicsView(PGGraphicsView):15 newMask = pyqtSignal(object)16 def __init__(self, parent, toolBar):17 super().__init__(parent)18 self.view = ViewBox(self)19 self.toolBar = toolBar20 self.toolBar.clearBtn.clicked.connect(self.clear)21 self.cursor = Cursor()22 self.gridItem = GridItem(textPen=None)23 self.gridItem.setZValue(10)24 self.view.addItem(self.gridItem)25 self.maskItem = MaskItem()26 self.view.addItem(self.maskItem)27 self.kernelGraphics = KernelGraphics(self.view, self.maskItem, self.toolBar)28 self.kernelGraphics.newStamp.connect(self.newStamp)29 self.mask = None30 self.initUI()31 def initUI(self):32 self.centralFrame = QFrame(self)33 self.centralFrame.setFrameShape(QFrame.NoFrame)34 self.centralFrame.setFrameShadow(QFrame.Raised)35 self.centralFrame.setContentsMargins(0, 0, 0, 0)36 self.centralFrame.setStyleSheet("border: none;")37 self.setObjectName("maskView")38 self.view.invertY()39 self.view.setAspectLocked(True)40 self.setCentralItem(self.view)41 self.setMinimumWidth(500)42 self.setMinimumHeight(300)43 self.centralLayout = QHBoxLayout(self.centralFrame)44 self.centralLayout.addWidget(self.centralFrame)45 self.centralLayout.setContentsMargins(0, 0, 0, 0)46 self.setLayout(self.centralLayout)47 self.show()48 """49 Called when new patient is loaded. Calls reset function50 ================== ===========================================================================51 **Arguments:**52 patient loaded patient53 ================== ===========================================================================54 """55 def newPatient(self, patient):56 self.reset()57 """58 Clears mask item and sets image to None59 """60 def reset(self):61 self.maskItem.clear()62 self.setCursor(self.cursor.DefaultCursor)63 """64 Resets binary mask array in mask item to all 0's65 """66 def clear(self):67 if self.maskItem.image is not None:68 self.maskItem.image[:, :] = 069 self.maskItem.updateImage()70 """71 Clears the existing mask. Called when the active series has changed.72 ================== ===========================================================================73 **Arguments:**74 series the series object75 ================== ===========================================================================76 """77 def seriesSelected(self, series):78 self.reset()79 if series is None:80 self.kernelGraphics.unsubscribe()81 return82 elif series.parentSequence.getSeriesByType("Phase") is None:83 self.kernelGraphics.unsubscribe()84 return85 images = []86 for image in series.images:87 images.append(image.pixel_array.T)88 images = np.array(images)89 mask = np.zeros((images.shape[1], images.shape[2]))90 self.maskItem.setImage(mask)91 self.view.addItem(self.maskItem)92 self.maskItem.updateImage()93 self.kernelGraphics.subscribe()94 """95 Called when the kernel stamper changes the existing mask.96 ================== ===========================================================================97 **Arguments:**98 mask numpy array mask99 100 **Signal:**101 newMask returns mask object102 ================== ===========================================================================103 """104 def newStamp(self, mask):105 self.mask = Mask()106 # adjust emitted mask107 adjustedMask = np.copy(mask)108 non_zero_indexes = np.nonzero(adjustedMask)109 nonzero_row = non_zero_indexes[0]110 nonzero_col = non_zero_indexes[1]111 for row, col in zip(nonzero_row, nonzero_col):112 if adjustedMask[row + 1, col] == 0:113 adjustedMask[row + 1, col] = 1114 if adjustedMask[row, col + 1] == 0:115 adjustedMask[row, col + 1] = 1116 if adjustedMask[row + 1, col + 1] == 0:117 adjustedMask[row + 1, col + 1] = 1118 _region = SegmentationRegion()119 _region.mask = adjustedMask120 self.mask.regions.append(_region)121 self.newMask.emit(self.mask)122 """123 Updates the mask to match the overlay. Overlay is assumed to be in image item coordinates.124 ================== ===========================================================================125 **Arguments:**126 overlay overlay object containing all independent overlays127 ================== ===========================================================================128 """129 def newOverlay(self, overlay):130 self.view.removeItem(self.maskItem)131 imageShape = (self.maskItem.image.shape[0], self.maskItem.image.shape[1])132 overallMask = np.empty(imageShape)133 self.mask = Mask()134 for region in overlay.regions:135 regionVertices = region.vertices136 regionCoordinates = [tuple([vertice.x(), vertice.y()]) for vertice in regionVertices]137 regionMask = Image.new('L', imageShape)138 ImageDraw.Draw(regionMask).polygon(regionCoordinates, outline=1, fill=1)139 regionMask = np.array(regionMask).T140 # adjust displayed mask to match overlay141 adjustedMask = np.copy(regionMask)142 non_zero_indexes = np.nonzero(adjustedMask)143 nonzero_row = non_zero_indexes[0]144 nonzero_col = non_zero_indexes[1]145 for row, col in zip(nonzero_row, nonzero_col):146 if adjustedMask[row + 1, col] == 0:147 adjustedMask[row, col] = 0148 if adjustedMask[row, col + 1] == 0:149 adjustedMask[row, col] = 0150 if adjustedMask[row + 1, col + 1] == 0:151 adjustedMask[row, col] = 0152 overallMask = adjustedMask + overallMask153 region.mask = regionMask154 self.mask.regions.append(region)155 overallMask[overallMask > 1] = 0156 self.maskItem.setImage(overallMask)157 self.view.addItem(self.maskItem)158 self.maskItem.updateImage()159 self.newMask.emit(self.mask)160 """161 Updates the mask to match the overlay. Overlay is assumed to be in image item coordinates.162 ================== ===========================================================================163 **Arguments:**164 vertices A list of tuples containing vertices from autosegmentation routine165 ================== ===========================================================================166 """167 def newAutoSeg(self, vertices):168 self.view.removeItem(self.maskItem)169 imageShape = (self.maskItem.image.shape[0], self.maskItem.image.shape[1])170 self.mask = Mask()171 overallMask = np.empty(imageShape)172 autoSegCoordinates = [tuple(vertice) for vertice in vertices]173 autoSegMask = Image.new('L', imageShape)174 ImageDraw.Draw(autoSegMask).polygon(autoSegCoordinates, outline=1, fill=1)175 autoSegMask = np.array(autoSegMask)176 overallMask = autoSegMask + overallMask177 overallMask[overallMask > 1] = 0178 _region = SegmentationRegion()179 _region.mask = overallMask180 self.mask.regions.append(_region)181 self.maskItem.setImage(overallMask)182 self.view.addItem(self.maskItem)183 self.maskItem.updateImage()184 self.newMask.emit(self.mask)185class Mask:186 def __init__(self):187 self.regions = []188"""189The pyqtgraph viewbox. The viewbox displays items.190"""191class ViewBox(pg.ViewBox):192 def __init__(self, parent):193 super().__init__()194 self.graphicsWidget = parent195 def initUI(self):196 self.setMouseEnabled(True)197 def mouseDragEvent(self, ev, axis=None):198 return199 def mouseClickEvent(self, ev):200 if ev.button() == Qt.RightButton:201 return202"""203The pyqtgraph image item. An image item stores the images.204"""205class MaskItem(pg.ImageItem):206 leftMousePressed = pyqtSignal(mouseEvents.MouseClickEvent)207 leftMouseDragged = pyqtSignal(mouseEvents.MouseDragEvent)208 def __init__(self, image=None):209 super().__init__(image=image)210 def mouseClickEvent(self, ev):211 if ev.button() == Qt.RightButton:212 return213 if ev.button() == Qt.LeftButton:214 self.leftMousePressed.emit(ev)215 def mouseDragEvent(self, ev):216 if ev.button() != Qt.LeftButton:217 return218 else:219 self.leftMouseDragged.emit(ev)220 def updateImage(self, *args, **kargs):221 super().updateImage(*args, **kargs)222"""223The pyqtgraph grid item. A grid item displays grid lines224"""225class GridItem(pg.GridItem):226 def __init__(self, textPen=None):...
KernelGraphics.py
Source:KernelGraphics.py
1from PyQt5.QtWidgets import QGraphicsObject2from PyQt5.QtCore import pyqtSignal3from pyqtgraph.GraphicsScene import mouseEvents4import numpy as np5import math6from scripts.UI.Cursor import Cursor7class KernelGraphics(QGraphicsObject):8 newStamp = pyqtSignal(object)9 def __init__(self, maskView, maskItem, toolBar):10 super().__init__()11 self.maskView = maskView12 self.maskItem = maskItem13 self.toolBar = toolBar14 self.setSize(self.toolBar.kernelBtn.kernelSize)15 self.toolBar.kernelBtn.kernelSelected.connect(self.setSize)16 self.eraseMode = False17 self.enabled = False18 def subscribe(self):19 self.unsubscribe()20 self.maskItem.leftMousePressed.connect(self.stampOnMouseAction)21 self.maskItem.leftMouseDragged.connect(self.stampOnMouseAction)22 def unsubscribe(self):23 try:24 self.maskItem.leftMousePressed.disconnect(self.stampOnMouseAction)25 except:26 pass27 try:28 self.maskItem.leftMouseDragged.disconnect(self.stampOnMouseAction)29 except:30 pass31 """32 Sets the size of the draw kernel.33 ================== ===========================================================================34 **Arguments:**35 kernelSize a 2d numpy array of 1's. size is defined by arrays shape36 ================== ===========================================================================37 """38 def setSize(self, kernelSize):39 cursor = Cursor()40 if kernelSize is None:41 self.maskView.graphicsWidget.setCursor(cursor.DefaultCursor)42 self.enabled = False43 return44 self.kernelSize = kernelSize45 self.kernel = np.tile(np.ones(self.kernelSize), (self.kernelSize, 1))46 self.maskItem.setDrawKernel(kernel=self.kernel,47 center=(math.floor(self.kernelSize / 2), math.floor(self.kernelSize / 2)),48 mode='set')49 self.maskView.graphicsWidget.setCursor(cursor.CrossCursor)50 self.enabled = True51 """52 Adds kernel at the current mouse position if mask is empty. Otherwise, erases existing kernel.53 ================== ===========================================================================54 **Arguments:**55 ev mouse event56 ================== ===========================================================================57 """58 def stampOnMouseAction(self, ev):59 if not self.enabled:60 return61 itemPos = ev.pos()62 viewPos = self.maskView.mapFromItemToView(self.maskItem, itemPos)63 i, j = viewPos.x(), viewPos.y()64 i = int(np.clip(i, 0, self.maskItem.image.shape[0] - 1))65 j = int(np.clip(j, 0, self.maskItem.image.shape[1] - 1))66 val = self.maskItem.image[i, j]67 bound_1 = math.floor(self.kernel.shape[0] / 2)68 bound_2 = math.ceil(self.kernel.shape[0] / 2)69 if type(ev) == mouseEvents.MouseDragEvent:70 if ev.isStart():71 if val == 1:72 self.eraseMode = True73 else:74 self.eraseMode = False75 if ev.isFinish():76 self.newStamp.emit(self.maskItem.image)77 if self.eraseMode:78 self.maskItem.image[(i - bound_1):(i + bound_2), (j - bound_1):(j + bound_2)] = 079 else:80 self.maskItem.drawAt(viewPos, ev)81 elif type(ev) == mouseEvents.MouseClickEvent:82 if val == 1:83 self.maskItem.image[(i - bound_1):(i + bound_2), (j - bound_1):(j + bound_2)] = 084 else:85 self.maskItem.drawAt(viewPos, ev)86 self.newStamp.emit(self.maskItem.image)...
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