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Optimizations, closes #1070 #1071

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87222a0
WIP: RP, draw new objects, etc
Teranis Apr 6, 2026
1cbb398
WIP: tracker opt
Teranis Apr 7, 2026
94c8bb4
feat: updated RP, updated tracking, updated lab modifications in many…
Teranis Apr 7, 2026
4ebeab5
WIP: fix regionprops local cutouts
Teranis Apr 7, 2026
5e9de08
WIP: Fix assignment update
Teranis Apr 8, 2026
5f3f62e
fix: set self.lab to avoid stale lab
Teranis Apr 9, 2026
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113 changes: 89 additions & 24 deletions cellacdc/annotate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import pandas as pd

from . import GUI_INSTALLED
from . import cellacdc_path, printl, ignore_exception
from . import cellacdc_path, printl, ignore_exception, debugutils

if GUI_INSTALLED:
from PIL import Image, ImageFont, ImageDraw
Expand Down Expand Up @@ -207,6 +207,45 @@ def __init__(self, *args, anchor=(0.5, 0.5), **kargs):
self.texts = []
self.annotData = []
self._anchor = anchor

def _rebuildSizes(self, bold=False):
if bold:
self.sizesBold = plot.get_symbol_sizes(
self.scalesBold, self.symbolsBold, self.fontSize
)
self._maxScaleBold = max(self.scalesBold.values(), default=None)
else:
self.sizesRegular = plot.get_symbol_sizes(
self.scalesRegular, self.symbolsRegular, self.fontSize
)
self._maxScaleRegular = max(self.scalesRegular.values(), default=None)

def _updateSizesForTexts(self, texts, bold=False):
if not texts:
return

if bold:
scales = self.scalesBold
sizes_attr = 'sizesBold'
max_scale_attr = '_maxScaleBold'
else:
scales = self.scalesRegular
sizes_attr = 'sizesRegular'
max_scale_attr = '_maxScaleRegular'

current_max_scale = getattr(self, max_scale_attr, None)
if current_max_scale is None:
self._rebuildSizes(bold=bold)
return

added_max_scale = max(scales[text] for text in texts)
if added_max_scale > current_max_scale:
self._rebuildSizes(bold=bold)
return

sizes = getattr(self, sizes_attr)
for text in texts:
sizes[text] = int(np.round(self.fontSize*current_max_scale/scales[text]))

def clearData(self):
self.setData([], [])
Expand Down Expand Up @@ -254,15 +293,28 @@ def initSymbols(self, allIDs, onlyIDs=False):
self.createSymbols(annotTexts)

def addSymbols(self, annotTexts, includeBold=True):
for text in annotTexts:
if includeBold:
self.symbolsBold[text] = self.getObjTextAnnotSymbol(
text, bold=True, initSizes=False
if includeBold:
missing_bold = [
text for text in annotTexts if text not in self.symbolsBold
]
if missing_bold:
symbolsBold, scalesBold = plot.texts_to_pg_scatter_symbols(
missing_bold, font=self.fontBold, return_scales=True
)
self.symbolsRegular[text] = self.getObjTextAnnotSymbol(
text, bold=True, initSizes=False
self.symbolsBold.update(symbolsBold)
self.scalesBold.update(scalesBold)
self._updateSizesForTexts(missing_bold, bold=True)

missing_regular = [
text for text in annotTexts if text not in self.symbolsRegular
]
if missing_regular:
symbolsRegular, scalesRegular = plot.texts_to_pg_scatter_symbols(
missing_regular, font=self.fontRegular, return_scales=True
)
self.initSizes(includeBold=includeBold)
self.symbolsRegular.update(symbolsRegular)
self.scalesRegular.update(scalesRegular)
self._updateSizesForTexts(missing_regular, bold=False)

def createSymbols(self, annotTexts, includeBold=True):
if includeBold:
Expand All @@ -281,12 +333,8 @@ def initSizes(self, includeBold=True):
includeBold = False

if includeBold:
self.sizesBold = plot.get_symbol_sizes(
self.scalesBold, self.symbolsBold, self.fontSize
)
self.sizesRegular = plot.get_symbol_sizes(
self.scalesRegular, self.symbolsRegular, self.fontSize
)
self._rebuildSizes(bold=True)
self._rebuildSizes(bold=False)

def setColors(self, colors):
self._colors = colors.copy()
Expand Down Expand Up @@ -325,7 +373,7 @@ def getObjTextAnnotSymbol(self, text, bold=False, initSizes=True):
symbols[text] = symbol
scales[text] = scale
if initSizes:
self.initSizes()
self._updateSizesForTexts([text], bold=bold)
return symbol

def grayOutAnnotations(self, IDsToSkip=None):
Expand All @@ -346,7 +394,7 @@ def grayOutAnnotations(self, IDsToSkip=None):
self.setBrush(brushes)
self.setPen(pens)

def highlightObject(self, obj):
def highlightObject(self, obj, rp=None, getObjCentroidFunc=None):
ID = obj.label
objIdx = None
for idx, objData in enumerate(self.data):
Expand All @@ -357,7 +405,14 @@ def highlightObject(self, obj):
objOpts = {
'text': str(ID), 'bold': True, 'color_name': 'new_object'
}
yc, xc = obj.centroid[-2:]
if rp is not None:
centroid = rp.get_centroid(obj.label)
else:
centroid = obj.centroid
if getObjCentroidFunc is not None:
yc, xc = getObjCentroidFunc(centroid)
else:
yc, xc = centroid[-2:]
pos = (int(xc), int(yc))
self.addObjAnnot(pos, draw=True, **objOpts)
return
Expand Down Expand Up @@ -504,13 +559,20 @@ def removeFromPlotItem(self, ax):
if hasattr(self.item, 'highlighterItem'):
ax.removeItem(self.item.highlighterItem)

def addObjAnnotation(self, obj, color_name, text, bold):
def addObjAnnotation(self, obj, color_name, text, bold, rp=None, getObjCentroidFunc=None):
objOpts = {
'text': text,
'bold': bold,
'color_name': color_name,
}
yc, xc = obj.centroid[-2:]
if rp is not None:
centroid = rp.get_centroid(obj.label)
else:
centroid = obj.centroid
if getObjCentroidFunc is not None:
yc, xc = getObjCentroidFunc(centroid)
else:
yc, xc = centroid[-2:]
pos = (int(xc), int(yc))
objData = self.item.addObjAnnot(pos, draw=True, **objOpts)
self.item.appendData(objData, objOpts['text'])
Expand Down Expand Up @@ -563,7 +625,8 @@ def setAnnotations(self, **kwargs):
isGenNumTreeAnnotation, posData.frame_i
)

yc, xc = getObjCentroidFunc(obj.centroid)
centroid = posData.rp.get_centroid(obj.label)
yc, xc = getObjCentroidFunc(centroid)
try:
rp_zslice = posData.zSlicesRp[currentZ]
obj_2d = rp_zslice[obj.label]
Expand Down Expand Up @@ -598,7 +661,8 @@ def setAnnotations(self, **kwargs):
'color_name': 'tracked_lost_object',
'bold': False,
}
yc, xc = obj.centroid[-2:]
centroid = prev_rp.get_centroid(obj.label)
yc, xc = getObjCentroidFunc(centroid)
pos = (int(xc), int(yc))
objData = self.item.addObjAnnot(pos, draw=False, **objOpts)
self.item.appendData(objData, objOpts['text'])
Expand All @@ -624,7 +688,8 @@ def setAnnotations(self, **kwargs):
'color_name': 'lost_object',
'bold': False,
}
yc, xc = getObjCentroidFunc(obj.centroid)
centroid = prev_rp.get_centroid(obj.label)
yc, xc = getObjCentroidFunc(centroid)
try:
pos = (int(xc), int(yc))
except Exception as err:
Expand All @@ -638,8 +703,8 @@ def setAnnotations(self, **kwargs):

self.item.draw()

def highlightObject(self, obj):
self.item.highlightObject(obj)
def highlightObject(self, obj, rp=None, getObjCentroidFunc=None):
self.item.highlightObject(obj, rp=None, getObjCentroidFunc=None)

def removeHighlightObject(self, obj):
self.item.removeHighlightObject(obj)
Expand Down
2 changes: 1 addition & 1 deletion cellacdc/apps.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7413,7 +7413,7 @@ def setPosData(self):
# self.img.setCurrentPosIndex(self.pos_i)
# self.img.minMaxValuesMapper = self.mainWin.img1.minMaxValuesMapper
self.origLab = self.posData.lab.copy()
self.origRp = skimage.measure.regionprops(self.origLab)
self.origRp = skimage.measure.regionprops(self.origLab) # why seperate rp here?
self.origObjs = {obj.label:obj for obj in self.origRp}

def valueChanged(self, value):
Expand Down
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