class Plugin(SlideRunnerPlugin.SlideRunnerPlugin):
version = 0.1
shortName = 'Secondary database visualization'
inQueue = Queue()
outQueue = Queue()
initialOpacity = 1.0
updateTimer = 0.1
outputType = SlideRunnerPlugin.PluginOutputType.RGB_IMAGE
description = 'Visualize secondary SlideRunner database'
pluginType = SlideRunnerPlugin.PluginTypes.WHOLESLIDE_PLUGIN
configurationList = list(
(SlideRunnerPlugin.FilePickerConfigurationEntry(uid='file',
name='Database file',
mask='*.sqlite'), ))
COLORS = [[0, 128, 0, 255], [128, 0, 0, 255], [0, 0, 128, 255],
[128, 128, 0, 255], [0, 128, 128, 255], [128, 128, 128, 255]]
def __init__(self, statusQueue: Queue):
self.statusQueue = statusQueue
self.annotationLabels = {}
self.secondaryDB = Database()
self.p = Thread(target=self.queueWorker, daemon=True)
self.p.start()
pass
def getAnnotationUpdatePolicy():
# This is important to tell SlideRunner that he needs to update for every change in position.
return SlideRunnerPlugin.AnnotationUpdatePolicy.UPDATE_ON_SLIDE_CHANGE
def queueWorker(self):
debugModule = False
quitSignal = False
oldFilename = ''
oldArchive = ''
oldSlide = ''
oldThres = -1
while not quitSignal:
job = SlideRunnerPlugin.pluginJob(self.inQueue.get())
print(job)
if (job.jobDescription ==
SlideRunnerPlugin.JobDescription.QUIT_PLUGIN_THREAD):
# signal to exit this thread
quitSignal = True
continue
if (job.configuration['file'] == oldArchive) and (job.slideFilename
== oldSlide):
continue
if not (os.path.exists(job.configuration['file'])):
continue
self.sendAnnotationLabelUpdate()
oldArchive = job.configuration['file']
oldSlide = job.slideFilename
self.secondaryDB.open(oldArchive)
self.annos = list()
self.annotationLabels = dict()
for key, (label, annoId,
col) in enumerate(self.secondaryDB.getAllClasses()):
self.annotationLabels[
annoId] = SlideRunnerPlugin.PluginAnnotationLabel(
0, '%s' % label, [*hex_to_rgb(col), 0])
pname, fname = os.path.split(job.slideFilename)
self.slideUID = self.secondaryDB.findSlideWithFilename(
fname, pname)
self.secondaryDB.loadIntoMemory(self.slideUID)
self.annos = list()
for annoId in self.secondaryDB.annotations.keys():
anno = self.secondaryDB.annotations[annoId]
anno.pluginAnnotationLabel = self.annotationLabels[
anno.agreedClass]
self.annos.append(anno)
self.sendAnnotationLabelUpdate()
self.updateAnnotations()
self.setProgressBar(-1)
self.setMessage('found %d annotations.' % len(self.annos))
def getAnnotations(self):
return self.annos
def getAnnotationLabels(self):
# sending default annotation labels
return [self.annotationLabels[k] for k in self.annotationLabels.keys()]
class Plugin(SlideRunnerPlugin.SlideRunnerPlugin):
version = 0.1
shortName = 'Mitosis Heatmap'
inQueue = Queue()
outQueue = Queue()
initialOpacity = 0.6
updateTimer = 0.1
outputType = SlideRunnerPlugin.PluginOutputType.BINARY_MASK
description = 'Show heatmap of mitotic figures in WSI'
pluginType = SlideRunnerPlugin.PluginTypes.WHOLESLIDE_PLUGIN
configurationList = list(
(SlideRunnerPlugin.FilePickerConfigurationEntry(
uid='file', name='Result file', mask='*.p;;*.txt;;*.p.bz2'),
SlideRunnerPlugin.FilePickerConfigurationEntry(uid='dbfile',
name='Database file',
mask='*.sqlite'),
SlideRunnerPlugin.PluginConfigurationEntry(uid='threshold',
name='Detection threshold',
initValue=0.75,
minValue=0.0,
maxValue=1.0),
SlideRunnerPlugin.ComboboxPluginConfigurationEntry(
uid='source',
name='Heatmap shows',
options=['Primary Database', 'Results', 'SecondaryDatabase'])))
COLORS = [[0, 128, 0, 255], [128, 0, 0, 255], [0, 0, 128, 255],
[128, 128, 0, 255], [0, 128, 128, 255], [128, 128, 128, 255]]
def __init__(self, statusQueue: Queue):
self.statusQueue = statusQueue
self.annotationLabels = {
'Detection':
SlideRunnerPlugin.PluginAnnotationLabel(0, 'Detection',
[0, 180, 0, 255]),
}
self.p = Thread(target=self.queueWorker, daemon=True)
self.p.start()
self.annos = []
self.downsampledMap = np.zeros((10, 10))
pass
def getAnnotationUpdatePolicy():
# This is important to tell SlideRunner that he needs to update for every change in position.
return SlideRunnerPlugin.AnnotationUpdatePolicy.UPDATE_ON_SLIDE_CHANGE
def queueWorker(self):
debugModule = False
quitSignal = False
oldFilename = ''
oldArchive = ''
oldSlide = ''
oldDBfile = ''
oldCoordinates = [-1, -1, -1, -1]
oldThres = -1
oldSource = -1
self.ds = 32
while not quitSignal:
job = SlideRunnerPlugin.pluginJob(self.inQueue.get())
print(job)
print(job.configuration)
if (job.jobDescription ==
SlideRunnerPlugin.JobDescription.QUIT_PLUGIN_THREAD):
# signal to exit this thread
quitSignal = True
continue
sourceChanged = job.configuration['source'] != oldSource
if (job.configuration['source'] == 0):
if not hasattr(job.openedDatabase, 'dbfilename'):
# DB not open yet
continue
job.configuration['dbfile'] = job.openedDatabase.dbfilename
dbfilechanged = job.configuration['dbfile'] != oldDBfile
if not (sourceChanged) and (
job.configuration['file'] == oldArchive
) and (job.configuration['threshold']
== oldThres) and (job.slideFilename == oldSlide) and np.all(
job.coordinates == oldCoordinates) and not (
dbfilechanged):
continue
if not (os.path.exists(job.configuration['file'])) and (
job.configuration['source'] == 1):
continue
self.sendAnnotationLabelUpdate()
fileChanged = job.configuration['file'] != oldArchive
oldDBfile = job.configuration['dbfile']
slideChanged = job.slideFilename != oldSlide
thresChanged = job.configuration['threshold'] != oldThres
oldArchive = job.configuration['file']
oldThres = job.configuration['threshold']
oldSlide = job.slideFilename
oldSource = job.configuration['source']
oldCoordinates = job.coordinates
[foo, self.ext] = os.path.splitext(oldArchive)
self.ext = self.ext.upper()
self.slideObj = openslide.open_slide(job.slideFilename)
if (fileChanged):
if (self.ext == '.P') or (
self.ext
== '.BZ2'): # Pickled format - results for many slides
if (self.ext == '.BZ2'):
self.resultsArchive = pickle.load(
bz2.BZ2File(oldArchive, 'rb'))
print('Opened bz2-compressed results container.')
else:
self.resultsArchive = pickle.load(
open(oldArchive, 'rb'))
print('Sourcechanged:', sourceChanged, 'dbfilechanged:',
dbfilechanged, (len(job.configuration['dbfile']) > 0))
if (sourceChanged or dbfilechanged or slideChanged) and (
(job.configuration['source'] == 2) or
(job.configuration['source']
== 0)) and (len(job.configuration['dbfile']) > 0):
self.slideObj = openslide.open_slide(job.slideFilename)
self.downsampledMap = np.zeros(
(int(self.slideObj.dimensions[1] / self.ds),
int(self.slideObj.dimensions[0] / self.ds)))
self.newDB = Database()
self.newDB.open(job.configuration['dbfile'])
allClasses = self.newDB.getAllClasses()
mitosisClass = -1
for clsname, clsuid, col in allClasses:
if (mitosisClass
== -1) and ('MITO' in clsname.upper()) and (
'LOOK' not in clsname.upper()):
mitosisClass = clsuid
pname, fname = os.path.split(job.slideFilename)
uid = self.newDB.findSlideWithFilename(fname, pname)
self.newDB.loadIntoMemory(uid)
for anno in self.newDB.annotations:
if (self.newDB.annotations[anno].agreedClass ==
mitosisClass):
annodet = self.newDB.annotations[anno]
self.downsampledMap[int(annodet.y1 / self.ds),
int(annodet.x1 / self.ds)] += 1
else:
self.setMessage('No DB open.')
if ((sourceChanged and job.configuration['source'] == 1) or
(slideChanged) or
(thresChanged)) and len(job.configuration['file']) > 0:
pname, fname = os.path.split(job.slideFilename)
print('Stage 6')
if (oldFilename is not fname) or (slideChanged):
# process slide
self.annos = list()
if (fname not in self.resultsArchive):
self.setMessage('Slide ' + str(fname) +
' not found in results file.')
print('List of files is: ', self.resultsArchive.keys())
continue
oldFilename = fname
uniqueLabels = np.unique(
np.array(self.resultsArchive[fname])[:, 4])
self.annotationLabels = dict()
for key, label in enumerate(uniqueLabels):
self.annotationLabels[
label] = SlideRunnerPlugin.PluginAnnotationLabel(
0, 'Class %d' % label,
self.COLORS[key % len(self.COLORS)])
if (job.configuration['source'] == 1):
self.downsampledMap = np.zeros(
(int(self.slideObj.dimensions[1] / self.ds),
int(self.slideObj.dimensions[0] / self.ds)))
print('Downsampled image: ', self.downsampledMap.shape)
for idx in range(len(self.resultsArchive[fname])):
row = self.resultsArchive[fname][idx]
if (row[5] > job.configuration['threshold']):
myanno = annotations.rectangularAnnotation(
uid=idx,
x1=row[0],
x2=row[2],
y1=row[1],
y2=row[3],
text='%.2f' % row[5],
pluginAnnotationLabel=self.annotationLabels[
row[4]])
if (job.configuration['source'] == 1):
self.downsampledMap[int(
(row[1] + row[3]) / 2 / self.ds),
int((row[0] + row[2]) / 2 /
self.ds)] += 1
self.annos.append(myanno)
self.sendAnnotationLabelUpdate()
elif (self.ext == '.TXT'): # Assume MS Coco format
self.annos = list()
self.resultsArchive = np.loadtxt(
oldArchive,
dtype={
'names':
('label', 'confidence', 'x', 'y', 'w', 'h'),
'formats': ('U30', 'f4', 'i4', 'i4', 'i4', 'i4')
},
skiprows=0,
delimiter=' ')
uniqueLabels = np.unique(self.resultsArchive['label'])
self.annotationLabels = dict()
for key, label in enumerate(uniqueLabels):
self.annotationLabels[
label] = SlideRunnerPlugin.PluginAnnotationLabel(
0, label, self.COLORS[key % len(self.COLORS)])
self.sendAnnotationLabelUpdate()
self.slideObj = openslide.open_slide(job.slideFilename)
self.ds = 32
if (job.configuration['source'] == 1):
self.downsampledMap = np.zeros(
(int(self.slideObj.dimensions[1] / self.ds),
int(self.slideObj.dimensions[0] / self.ds)))
print('Downsampled image: ', self.downsampledMap.shape)
for idx in range(len(self.resultsArchive)):
row = self.resultsArchive[idx]
if (row[5] > job.configuration['threshold']):
if (job.configuration['source'] == 1):
self.downsampledMap[int(
(row['y'] - row['h'] / 2) / self.ds),
int((row['x'] -
row['w'] / 2) /
self.ds)] += 1
myanno = annotations.rectangularAnnotation(
uid=idx,
x1=row['x'],
x2=row['y'],
y1=row['x'] + row['w'],
y2=row['y'] + row['h'],
text='%.2f' % row['confidence'],
pluginAnnotationLabel=self.annotationLabels[
row['label']])
self.annos.append(myanno)
print('returning overlay...')
A = 2.37 # mm^2
W_hpf_microns = np.sqrt(A * 4 / 3) * 1000 # in microns
H_hpf_microns = np.sqrt(A * 3 / 4) * 1000 # in microns
micronsPerPixel = self.slideObj.properties[
openslide.PROPERTY_NAME_MPP_X]
W_hpf = int(W_hpf_microns / float(micronsPerPixel))
H_hpf = int(H_hpf_microns / float(micronsPerPixel))
W_x = int(W_hpf / self.ds)
W_y = int(H_hpf / self.ds)
kernel = np.ones((W_y, W_x), np.float32)
mitoticCount = cv2.filter2D(self.downsampledMap, -1, kernel)
coords_ds = np.int16(np.array(job.coordinates) / self.ds)
centerImg = cv2.getRectSubPix(
np.float32(mitoticCount[:, :, None]),
patchSize=(coords_ds[2], coords_ds[3]),
center=(coords_ds[0] + coords_ds[2] * 0.5,
coords_ds[1] + coords_ds[3] * 0.5))
resized = cv2.resize(centerImg,
dsize=(job.currentImage.shape[1],
job.currentImage.shape[0]))
self.returnImage(resized)
self.updateAnnotations()
self.setProgressBar(-1)
self.setMessage('found %d annotations.' % len(self.annos))
def getAnnotations(self):
return self.annos
def getAnnotationLabels(self):
# sending default annotation labels
return [self.annotationLabels[k] for k in self.annotationLabels.keys()]
class Plugin(SlideRunnerPlugin.SlideRunnerPlugin):
version = 0.1
shortName = 'Object Detection Results'
inQueue = Queue()
outQueue = Queue()
initialOpacity = 1.0
updateTimer = 0.1
outputType = SlideRunnerPlugin.PluginOutputType.NO_OVERLAY
description = 'Show unpickled object detection results'
pluginType = SlideRunnerPlugin.PluginTypes.WHOLESLIDE_PLUGIN
configurationList = list((
SlideRunnerPlugin.FilePickerConfigurationEntry(uid='file',
name='Result file',
mask='*.p;;*.txt'),
SlideRunnerPlugin.PluginConfigurationEntry(uid='threshold',
name='Detection threshold',
initValue=0.75,
minValue=0.0,
maxValue=1.0),
))
COLORS = [[0, 128, 0, 255], [128, 0, 0, 255], [0, 0, 128, 255],
[128, 128, 0, 255], [0, 128, 128, 255], [128, 128, 128, 255]]
def __init__(self, statusQueue: Queue):
self.statusQueue = statusQueue
self.annotationLabels = {
'Detection':
SlideRunnerPlugin.PluginAnnotationLabel(0, 'Detection',
[0, 180, 0, 255]),
}
self.p = Thread(target=self.queueWorker, daemon=True)
self.p.start()
pass
def getAnnotationUpdatePolicy():
# This is important to tell SlideRunner that he needs to update for every change in position.
return SlideRunnerPlugin.AnnotationUpdatePolicy.UPDATE_ON_SLIDE_CHANGE
def queueWorker(self):
debugModule = False
quitSignal = False
oldFilename = ''
oldArchive = ''
oldSlide = ''
oldThres = -1
while not quitSignal:
job = SlideRunnerPlugin.pluginJob(self.inQueue.get())
print(job)
print(job.configuration)
if (job.jobDescription ==
SlideRunnerPlugin.JobDescription.QUIT_PLUGIN_THREAD):
# signal to exit this thread
quitSignal = True
continue
if (job.configuration['file']
== oldArchive) and (job.configuration['threshold']
== oldThres) and (job.slideFilename
== oldSlide):
continue
if not (os.path.exists(job.configuration['file'])):
continue
print('Performing label update')
self.sendAnnotationLabelUpdate()
oldArchive = job.configuration['file']
oldThres = job.configuration['threshold']
oldSlide = job.slideFilename
[foo, self.ext] = os.path.splitext(oldArchive)
self.ext = self.ext.upper()
self.annos = list()
if (self.ext == '.P'): # Pickled format - results for many slides
self.resultsArchive = pickle.load(open(oldArchive, 'rb'))
pname, fname = os.path.split(job.slideFilename)
fnamewithfolder = pname.split(os.sep)[-1] + os.sep + fname
if (oldFilename is not fname):
# process slide
if (fname not in self.resultsArchive) and (
fnamewithfolder not in self.resultsArchive):
self.setMessage('Slide ' + str(fname) +
' not found in results file.')
print('List is:', self.resultsArchive.keys())
continue
if (fnamewithfolder in self.resultsArchive):
fname = fnamewithfolder
oldFilename = fname
uniqueLabels = np.unique(
np.array(self.resultsArchive[fname])[:, 4])
self.annotationLabels = dict()
for key, label in enumerate(uniqueLabels):
self.annotationLabels[
label] = SlideRunnerPlugin.PluginAnnotationLabel(
key, 'Class %d' % label,
self.COLORS[key % len(self.COLORS)])
for idx in range(len(self.resultsArchive[fname])):
row = self.resultsArchive[fname][idx]
if (row[5] > job.configuration['threshold']):
myanno = annotations.rectangularAnnotation(
uid=idx,
x1=row[0],
x2=row[2],
y1=row[1],
y2=row[3],
text='%.2f' % row[5],
pluginAnnotationLabel=self.annotationLabels[
row[4]])
self.annos.append(myanno)
self.sendAnnotationLabelUpdate()
elif (self.ext == '.TXT'): # Assume MS Coco format
self.resultsArchive = np.loadtxt(
oldArchive,
dtype={
'names': ('label', 'confidence', 'x', 'y', 'w', 'h'),
'formats': ('U30', 'f4', 'i4', 'i4', 'i4', 'i4')
},
skiprows=0,
delimiter=' ')
uniqueLabels = np.unique(self.resultsArchive['label'])
self.annotationLabels = dict()
for key, label in enumerate(uniqueLabels):
self.annotationLabels[
label] = SlideRunnerPlugin.PluginAnnotationLabel(
key, label, self.COLORS[key % len(self.COLORS)])
self.sendAnnotationLabelUpdate()
for idx in range(len(self.resultsArchive)):
row = self.resultsArchive[idx]
if (row[5] > job.configuration['threshold']):
myanno = annotations.rectangularAnnotation(
uid=idx,
x1=row['x'],
y1=row['y'],
x2=row['x'] + row['w'],
y2=row['y'] + row['h'],
text='%.2f' % row['confidence'],
pluginAnnotationLabel=self.annotationLabels[
row['label']])
self.annos.append(myanno)
self.updateAnnotations()
self.setProgressBar(-1)
self.setMessage('found %d annotations.' % len(self.annos))
def getAnnotations(self):
return self.annos
def getAnnotationLabels(self):
# sending default annotation labels
return [self.annotationLabels[k] for k in self.annotationLabels.keys()]
class Plugin(SlideRunnerPlugin.SlideRunnerPlugin):
version = 0.1
shortName = 'Re-Stained WSI Registration (Jiang et al.)'
inQueue = Queue()
outQueue = Queue()
updateTimer=0.5
outputType = SlideRunnerPlugin.PluginOutputType.RGB_OVERLAY
description = 'Apply Jiang''s method for WSI co-registration'
pluginType = SlideRunnerPlugin.PluginTypes.IMAGE_PLUGIN
configurationList = list((
SlideRunnerPlugin.FilePickerConfigurationEntry(uid='file', name='Second WSI', mask='*.svs;;*.tif'),
SlideRunnerPlugin.PluginConfigurationEntry(uid='xoffset', name='X Offset', initValue=0, minValue=-2000, maxValue=2000.0),
SlideRunnerPlugin.PluginConfigurationEntry(uid='yoffset', name='Y Offset', initValue=0, minValue=-2000, maxValue=2000.0),
SlideRunnerPlugin.PushbuttonPluginConfigurationEntry(uid='match',name='Match')
))
def __init__(self, statusQueue:Queue):
self.statusQueue = statusQueue
self.p = Thread(target=self.queueWorker, daemon=True)
self.p.start()
pass
def queueWorker(self):
oldwsi=None
quitSignal=False
sl=None
detected_offset = None
sl_main = None
while not quitSignal:
job = SlideRunnerPlugin.pluginJob(self.inQueue.get())
image = job.currentImage
mainWSI = job.slideFilename
if 'file' not in job.configuration:
continue
if (job.configuration['file'] != oldwsi) and (job.configuration['file']!='') and job.configuration['file']:
sl = openslide.open_slide(job.configuration['file'])
if (mainWSI):
sl_main = openslide.open_slide(mainWSI)
if (job.trigger is not None) and job.trigger.uid=='match':
print('Trigger: ',job.trigger)
self.setProgressBar(0)
self.setMessage('Calculating optimum offset')
tissue_detector = TissueDetector("LAB_Threshold", threshold=80) # option 1
matcher_parameters = MatcherParameters() # use the default parameters
matcher = WSI_Matcher(tissue_detector, matcher_parameters)
detected_offset = matcher.match(mainWSI, job.configuration['file'])
self.setProgressBar(-1)
updateConfig = list()
updateConfig.append(SlideRunnerPlugin.PluginConfigUpdateEntry(SlideRunnerPlugin.PluginConfigurationType.SLIDER_WITH_FLOAT_VALUE, uid='xoffset', value=detected_offset[0]))
updateConfig.append(SlideRunnerPlugin.PluginConfigUpdateEntry(SlideRunnerPlugin.PluginConfigurationType.SLIDER_WITH_FLOAT_VALUE, uid='yoffset', value=detected_offset[1]))
self.updateConfiguration(SlideRunnerPlugin.PluginConfigUpdate(updateConfig))
if (sl) and (sl_main):
self.setProgressBar(0)
print('Reading from: ',job)
zoomValue=job.coordinates[3]/job.currentImage.shape[0]
print('Zoom value: ',zoomValue)
act_level = np.argmin(np.abs(np.asarray(sl.level_downsamples)-zoomValue))
closest_ds = sl_main.level_downsamples[np.argmin(np.abs(np.asarray(sl_main.level_downsamples)-zoomValue))]
offset = (job.configuration['xoffset'],job.configuration['yoffset'])
if (detected_offset is not None):
offset=detected_offset
offset_scaled = [int(x/closest_ds) for x in offset]
print('Scaled offset is: ',offset_scaled)
imgarea_w=job.coordinates[2:4]
size_im = (int(imgarea_w[0]/closest_ds), int(imgarea_w[1]/closest_ds))
print('Image size: ',size_im)
location = [int(x+y) for x,y in zip(job.coordinates[0:2],offset)]
print('Location (original):',job.coordinates[0:2])
print('Location (offset): ',location)
img = sl.read_region(location=location, level=act_level, size=size_im)
img = np.array(img.resize((job.currentImage.shape[1],job.currentImage.shape[0] )))
self.returnImage(img, job.procId)
self.setMessage('Align done.')
self.setProgressBar(-1)
if (job.jobDescription == SlideRunnerPlugin.JobDescription.QUIT_PLUGIN_THREAD):
# signal to exit this thread
quitSignal=True
continue
print('OTSU plugin: received 1 image from queue')
