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perf: faster lost objects and lost tracked objects contours
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@ElpadoCan
ElpadoCan committed Feb 3, 2025
1 parent 0c75d55 commit 76102cb
Showing 1 changed file with 150 additions and 49 deletions.
199 changes: 150 additions & 49 deletions cellacdc/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4908,6 +4908,13 @@ def _gui_createGraphicsItems(self):
self.logger.info(f'Creating graphical items...')

self.ax1_contoursImageItem = pg.ImageItem()

self.ax1_lostObjImageItem = pg.ImageItem()
self.ax2_lostObjImageItem = pg.ImageItem()

self.ax1_lostTrackedObjImageItem = pg.ImageItem()
self.ax2_lostTrackedObjImageItem = pg.ImageItem()

self.ax1_oldMothBudLinesItem = pg.ScatterPlotItem(
symbol='s', pxMode=False, brush=self.oldMothBudLineBrush,
size=self.mothBudLineWeight, pen=None
Expand Down Expand Up @@ -8037,7 +8044,6 @@ def gui_mousePressEventImg1(self, event):
self.warnEditingWithCca_df('Add new ID with curvature tool')
self.clearCurvItems()
self.curvTool_cb(True)
t1 = time.perf_counter()

elif left_click and canWand:
x, y = event.pos().x(), event.pos().y()
Expand Down Expand Up @@ -8455,6 +8461,8 @@ def annotate_unknown_lineage_action(self, posData, event, ydata, xdata):

def gui_addCreatedAxesItems(self):
self.ax1.addItem(self.ax1_contoursImageItem)
self.ax1.addItem(self.ax1_lostObjImageItem)
self.ax1.addItem(self.ax1_lostTrackedObjImageItem)
self.ax1.addItem(self.ax1_oldMothBudLinesItem)
self.ax1.addItem(self.ax1_newMothBudLinesItem)
self.ax1.addItem(self.ax1_lostObjScatterItem)
Expand All @@ -8463,6 +8471,8 @@ def gui_addCreatedAxesItems(self):
self.ax1.addItem(self.yellowContourScatterItem)

self.ax2.addItem(self.ax2_contoursImageItem)
self.ax2.addItem(self.ax2_lostObjImageItem)
self.ax2.addItem(self.ax2_lostTrackedObjImageItem)
self.ax2.addItem(self.ax2_oldMothBudLinesItem)
self.ax2.addItem(self.ax2_newMothBudLinesItem)
self.ax2.addItem(self.ax2_lostObjScatterItem)
Expand Down Expand Up @@ -9345,10 +9355,14 @@ def getClickedID(self, xdata, ydata, text=''):
else:
ID = clickedBkgrID.EntryID
return ID


# @exec_time
def applyEditID(
self, clickedID, currentIDs, oldIDnewIDMapper, clicked_x, clicked_y
):

t0 = time.perf_counter()

posData = self.data[self.pos_i]

# Ask to propagate change to all future visited frames
Expand All @@ -9358,6 +9372,8 @@ def applyEditID(
posData.UndoFutFrames_EditID, posData.applyFutFrames_EditID,
applyTrackingB=True
)

t1 = time.perf_counter()

if UndoFutFrames is None:
return
Expand Down Expand Up @@ -9402,12 +9418,12 @@ def applyEditID(
posData.editID_info.append((y, x, new_ID))

self.updateAssignedObjsAcdcTrackerSecondStep(new_ID)

# Update rps
self.update_rp()

# Since we manually changed an ID we don't want to repeat tracking
self.setAllTextAnnotations()
self.setAllTextAnnotations()
self.highlightLostNew()
# self.checkIDsMultiContour()

Expand All @@ -9418,8 +9434,8 @@ def applyEditID(
self.fixCcaDfAfterEdit('Edit ID')
self.updateAllImages()
else:
self.warnEditingWithCca_df('Edit ID')

self.warnEditingWithCca_df('Edit ID', update_images=False)
if not self.editIDbutton.findChild(QAction).isChecked():
self.editIDbutton.setChecked(False)

Expand Down Expand Up @@ -11203,12 +11219,9 @@ def addDelROI(self, event):
self.fixCcaDfAfterEdit('Delete IDs using ROI')
self.updateAllImages()
else:
cancelled_str = self.warnEditingWithCca_df(
self.warnEditingWithCca_df(
'Delete IDs using ROI', get_cancelled=True
)
if cancelled_str == 'cancelled':
self.roi_to_del = roi
self.removeDelROI(None)

def replacePolyLineRoiWithLineRoi(self, roi):
roi = self.polyLineRoi
Expand Down Expand Up @@ -12979,6 +12992,10 @@ def keepIDs_cb(self, checked):
self.labelsLayerRightImg.setOpacity(alpha)
self.ax1_contoursImageItem.setOpacity(1.0)
self.ax2_contoursImageItem.setOpacity(1.0)
self.ax1_lostObjImageItem.setOpacity(1.0)
self.ax2_lostObjImageItem.setOpacity(1.0)
self.ax1_lostTrackedObjImageItem.setOpacity(1.0)
self.ax2_lostTrackedObjImageItem.setOpacity(1.0)

self.keepIDsToolbar.setVisible(checked)
self.highlightedIDopts = None
Expand Down Expand Up @@ -13552,7 +13569,7 @@ def keyPressEvent(self, ev):
return

if ev.key() == Qt.Key_Q and self.debug:
printl(self.zSliceScrollBar.value())
printl(np.nonzero(self.lostObjContoursImage))
pass

if not self.isDataLoaded:
Expand Down Expand Up @@ -18123,6 +18140,8 @@ def clearAx2Items(self, onlyHideText=False):
self.ax2_binnedIDs_ScatterPlot.clear()
self.ax2_ripIDs_ScatterPlot.clear()
self.ax2_contoursImageItem.clear()
self.ax2_lostObjImageItem.clear()
self.ax2_lostTrackedObjImageItem.clear()
self.textAnnot[1].clear()
self.ax2_newMothBudLinesItem.setData([], [])
self.ax2_oldMothBudLinesItem.setData([], [])
Expand All @@ -18140,6 +18159,8 @@ def clearAx1Items(self, onlyHideText=False):
self.searchedIDitemLeft.clear()
self.searchedIDitemRight.clear()
self.ax1_contoursImageItem.clear()
self.ax1_lostObjImageItem.clear()
self.ax1_lostTrackedObjImageItem.clear()
self.textAnnot[0].clear()
self.ax1_newMothBudLinesItem.setData([], [])
self.ax1_oldMothBudLinesItem.setData([], [])
Expand Down Expand Up @@ -22502,6 +22523,22 @@ def initContoursImage(self):

self.contoursImage = np.zeros((Y, X, 4), dtype=np.uint8)

def initLostObjContoursImage(self):
posData = self.data[self.pos_i]
z_slice = self.z_lab()
img = posData.img_data[posData.frame_i]
Y, X = img[z_slice].shape[-2:]

self.lostObjContoursImage = np.zeros((Y, X, 4), dtype=np.uint8)

def initLostTrackedObjContoursImage(self):
posData = self.data[self.pos_i]
z_slice = self.z_lab()
img = posData.img_data[posData.frame_i]
Y, X = img[z_slice].shape[-2:]

self.lostTrackedObjContoursImage = np.zeros((Y, X, 4), dtype=np.uint8)

def initManualBackgroundImage(self):
posData = self.data[self.pos_i]
if hasattr(posData, 'lab'):
Expand Down Expand Up @@ -23876,7 +23913,9 @@ def warnEditingWithCca_df(
if update_images:
self.updateAllImages()
return True

action = self.warnEditingWithAnnotActions.get(editTxt, None)
printl(action, update_images)
if action is not None:
if not action.isChecked():
if update_images:
Expand Down Expand Up @@ -24305,6 +24344,18 @@ def getContoursImageItem(self, ax):
else:
return self.ax2_contoursImageItem

def getLostObjImageItem(self, ax):
if ax == 0:
return self.ax1_lostObjImageItem
else:
return self.ax1_lostTrackedObjImageItem

def getLostTrackedObjImageItem(self, ax):
if ax == 0:
return self.ax1_lostTrackedObjImageItem
else:
return self.ax2_lostTrackedObjImageItem

def setManualBackgroundImage(self):
if not self.manualBackgroundButton.isChecked():
return
Expand Down Expand Up @@ -24406,7 +24457,7 @@ def updateContoursImage(self, ax, delROIsIDs=None):
self.initContoursImage()
else:
self.contoursImage[:] = 0

contours = []
for obj in skimage.measure.regionprops(self.currentLab2D):
obj_contours = self.getObjContours(obj, all_external=True)
Expand Down Expand Up @@ -24452,11 +24503,83 @@ def setTrackedLostObjectContour(self, obj):
self.ax1_lostTrackedScatterItem.addPoints(xx, yy, data=data)
self.ax2_lostTrackedScatterItem.addPoints(xx, yy)

def getNearestLostObjID(self, y, x):
xx, yy = self.ax2_lostObjScatterItem.getData()
if xx is None:
def updateLostContoursImage(self, ax, delROIsIDs=None):
imageItem = self.getLostObjImageItem(ax)
if imageItem is None:
return

if not hasattr(self, 'lostObjContoursImage'):
self.initLostObjContoursImage()
else:
self.lostObjContoursImage[:] = 0

if delROIsIDs is None:
delROIsIDs = set()

posData = self.data[self.pos_i]
prev_rp = posData.allData_li[posData.frame_i-1]['regionprops']
prev_IDs_idxs = posData.allData_li[posData.frame_i-1]['IDs_idxs']
contours = []
for lostID in posData.lost_IDs:
if lostID in delROIsIDs:
continue

obj = prev_rp[prev_IDs_idxs[lostID]]
if not self.isObjVisible(obj.bbox):
continue

obj_contours = self.getObjContours(obj, all_external=True)
contours.extend(obj_contours)

self.drawLostObjContoursImage(imageItem, contours)

def drawLostObjContoursImage(self, imageItem, contours):
thickness = 1
color = (255, 165, 0, 255) # orange
img = self.lostObjContoursImage
cv2.drawContours(img, contours, -1, color, thickness)
imageItem.setImage(img)

def updateLostTrackedContoursImage(self, ax, delROIsIDs=None):
imageItem = self.getLostTrackedObjImageItem(ax)
if imageItem is None:
return

if not hasattr(self, 'lostTrackedObjContoursImage'):
self.initLostTrackedObjContoursImage()
else:
self.lostTrackedObjContoursImage[:] = 0

if delROIsIDs is None:
delROIsIDs = set()

posData = self.data[self.pos_i]
tracked_lost_IDs = self.getTrackedLostIDs()
prev_rp = posData.allData_li[posData.frame_i-1]['regionprops']
prev_IDs_idxs = posData.allData_li[posData.frame_i-1]['IDs_idxs']
contours = []
for tracked_lost_ID in tracked_lost_IDs:
if tracked_lost_ID in delROIsIDs:
continue

obj = prev_rp[prev_IDs_idxs[tracked_lost_ID]]
if not self.isObjVisible(obj.bbox):
continue

obj_contours = self.getObjContours(obj, all_external=True)
contours.extend(obj_contours)

self.drawLostTrackedObjContoursImage(imageItem, contours)

def drawLostTrackedObjContoursImage(self, imageItem, contours):
thickness = 1
color = (0, 255, 0, 255) # green
img = self.lostTrackedObjContoursImage
cv2.drawContours(img, contours, -1, color, thickness)
imageItem.setImage(img)

def getNearestLostObjID(self, y, x):
yy, xx, _ = np.nonzero(self.lostObjContoursImage)
if len(xx) == 0:
return

Expand Down Expand Up @@ -24651,6 +24774,14 @@ def setAllContoursImages(self, delROIsIDs=None):
self.updateContoursImage(ax=0, delROIsIDs=delROIsIDs)
self.updateContoursImage(ax=1, delROIsIDs=delROIsIDs)

def setAllLostObjContoursImage(self, delROIsIDs=None):
self.updateLostContoursImage(ax=0, delROIsIDs=None)
self.updateLostContoursImage(ax=1, delROIsIDs=None)

def setAllLostTrackedObjContoursImage(self, delROIsIDs=None):
self.updateLostTrackedContoursImage(ax=0, delROIsIDs=None)
self.updateLostTrackedContoursImage(ax=1, delROIsIDs=None)

def nextFrameImage(self, current_frame_i=None):
if not self.labelsGrad.showNextFrameAction.isEnabled():
return
Expand Down Expand Up @@ -24984,59 +25115,29 @@ def highlightNewIDs_ccaFailed(self, IDsWithIssue, rp=None):
continue
self.setCcaIssueContour(obj)

# @exec_time
def highlightLostNew(self):
if self.modeComboBox.currentText() == 'Viewer':
return

posData = self.data[self.pos_i]
delROIsIDs = self.getDelRoisIDs()

for obj in posData.rp:
ID = obj.label
if ID not in posData.new_IDs:
continue
if ID in delROIsIDs:
continue

if not self.isObjVisible(obj.bbox):
continue

self.addObjContourToContoursImage(
obj=obj, ax=0, thickness=self.contLineWeight+1
)
self.addObjContourToContoursImage(
obj=obj, ax=1, thickness=self.contLineWeight+1
)

self.setAllContoursImages(delROIsIDs=delROIsIDs)
if posData.frame_i == 0:
return

if not self.annotLostObjsToggle.isChecked():
return

tracked_lost_IDs = self.getTrackedLostIDs()

prev_rp = posData.allData_li[posData.frame_i-1]['regionprops']

if prev_rp is None:
return

for obj in prev_rp:

if obj.label in tracked_lost_IDs:
self.setTrackedLostObjectContour(obj)
self.setAllLostObjContoursImage(delROIsIDs=delROIsIDs)
self.setAllLostTrackedObjContoursImage(delROIsIDs=delROIsIDs)

if obj.label not in posData.lost_IDs:
continue

if obj.label in delROIsIDs:
continue

if not self.isObjVisible(obj.bbox):
continue

self.setLostObjectContour(obj)

if self.copyContourButton.isChecked():
self.addLostObjsToImage()

Expand Down

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