From 8611f68b7c64085a07811f16d9e0c7aae8fc2c57 Mon Sep 17 00:00:00 2001
From: Valentin Valls <valentin.valls@esrf.fr>
Date: Tue, 8 Oct 2024 10:36:50 +0200
Subject: [PATCH] Remove blank lines
---
SampleAlignment/SampleAlignment.py | 198 ++++++++++++++---------------
SampleAlignment/TomoSampleAlign.py | 62 ++++-----
SamplesDS/TomoSample.py | 14 +-
3 files changed, 137 insertions(+), 137 deletions(-)
diff --git a/SampleAlignment/SampleAlignment.py b/SampleAlignment/SampleAlignment.py
index beb90f5..323d9ea 100644
--- a/SampleAlignment/SampleAlignment.py
+++ b/SampleAlignment/SampleAlignment.py
@@ -19,13 +19,13 @@ import math
class OffsetsCalculation:
-
+
def __init__(self,resolution,imageDir,stand,borderType):
-
+
#monkey.patch_all(thread=False)
self.totalProcessingTime = 0
-
+
#self.sampleSizeX = sampleSize[0]
#self.sampleSizeY = sampleSize[1]
#self.sampleSizeZ = sampleSize[2]
@@ -36,34 +36,34 @@ class OffsetsCalculation:
self.pathImg = '/users/muzelle/Desktop/success2/007_HA-300_6.5_NUS2__004_/007_HA-300_6.5_NUS2__004_0000.edf'
self.pathFlat = '/users/muzelle/Desktop/success2/007_HA-300_6.5_NUS2__004_/refHST0000.edf'
self.pathDark = '/users/muzelle/Desktop/success2/007_HA-300_6.5_NUS2__004_/dark.edf'
-
+
self.resolution = resolution
-
+
self.stand = stand
-
+
self.borderType = borderType
-
+
self.img = None
self.flat = None
self.dark = None
-
+
self.dispImg = None
self.intImg = None
-
+
self.centImgY = None
self.centImgX = None
-
+
self.centerY = None
self.centerX = None
-
+
self.leftBorder = None
self.rightBorder = None
-
+
self.borderDetected = "false"
-
+
def imagesOpening(self):
-
+
start = time.time()
self.img = fabio.open(self.pathImg)
@@ -72,43 +72,43 @@ class OffsetsCalculation:
self.centImgY = int(self.img.data.shape[0]/2)
self.centImgX = int(self.img.data.shape[1]/2)
-
+
imagesOpeningTime = time.time()-start
self.totalProcessingTime += imagesOpeningTime
print("Time to open images: "+str(imagesOpeningTime))
-
-
+
+
def imageContrastEnhancement(self):
-
+
start = time.time()
-
+
filtImg = np.subtract(self.img.data,self.dark.data).astype(np.float32)
filtImgFlat = np.subtract(self.flat.data,self.dark.data).astype(np.float32)
corrImg = np.divide(filtImg,filtImgFlat).astype(np.float32)
corrImg[corrImg < 0] = 0
-
+
enhImg = cv2.normalize(corrImg, None, 0, 255, cv2.NORM_MINMAX).astype(np.uint8)
-
+
self.img = corrImg
-
+
imageContrastEnhancementTime = time.time()-start
self.totalProcessingTime += imageContrastEnhancementTime
print("Time to enhance image contrast: "+str(imageContrastEnhancementTime))
-
+
def imageFiltering(self):
-
+
start = time.time()
blurImg = cv2.bilateralFilter(self.img,9,75,75)
blurImg = cv2.normalize(blurImg, None, 0, 255, cv2.NORM_MINMAX).astype(np.uint8)
-
+
self.img = blurImg
self.dispImg = blurImg
-
+
imageFilteringTime = time.time()-start
self.totalProcessingTime += imageFilteringTime
print("Time to filter image: "+str(imageFilteringTime))
-
+
def edgesDetection(self):
start = time.time()
@@ -122,13 +122,13 @@ class OffsetsCalculation:
thr = np.median(edges)*1.33
edges = np.uint8(edges < -thr)
-
+
#measures = cv2.connectedComponentsWithStats(edges, 8, cv2.CV_32S)
-
+
#labImg = measures[1]
-
+
#areas = measures[2][:,cv2.CC_STAT_AREA]
-
+
labImg = measure.label(edges, neighbors=8, background=0)
labImg += 1
@@ -142,149 +142,149 @@ class OffsetsCalculation:
labImg = morphology.remove_small_objects(labImg,noise,in_place=True)
edges = np.uint8(labImg > 0)
-
+
#self.dispImg[edges > 0] = 0
-
+
#savedImg = fabio.edfimage.EdfImage()
#savedImg.data = self.dispImg
#savedImg.write('/segfs/tango/tmp/clemence/SampleAlignment/edgesDetected.edf')
-
+
self.img = labImg
-
+
edgesDetectionTime = time.time()-start
self.totalProcessingTime += edgesDetectionTime
print("Time to find edges: "+str(edgesDetectionTime))
-
-
+
+
def sampleCenterXCalculation(self):
-
+
start = time.time()
-
+
props = measure.regionprops(self.img,self.dispImg)
-
+
centroids = [(p.centroid[0],p.centroid[1]) for p in props if p.max_intensity > 200]
-
+
if len(centroids) != 0:
self.borderDetected = "true"
-
+
if self.stand == 'absent':
-
-
+
+
if self.borderType == 'straight':
-
+
self.leftBorder = np.min(centroids,axis=0)[1]
self.rightBorder = np.max(centroids,axis=0)[1]
-
+
self.centerX = int((self.rightBorder - self.leftBorder)/2+self.leftBorder)
-
+
if self.borderType == 'irregular':
-
+
edges = self.img > 0
-
+
self.leftBorder = np.min(centroids,axis=0)[1]
-
+
print('left border: '+str(self.leftBorder))
-
+
self.rightBorder = np.max(centroids,axis=0)[1]
-
+
print('right border: '+str(self.rightBorder))
-
+
self.centerX = int(np.mean([(np.min(np.where(edges[raw,:])[0])+np.max(np.where(edges[raw,:])[0]))/2
for raw in range(edges.shape[0])
if len(np.where(edges[raw,:])[0]) != 0
and (np.max(np.where(edges[raw,:])[0])-np.min(np.where(edges[raw,:])[0])) > 200]
))
-
+
if self.borderType == 'oblique':
-
+
edges = self.img > 0
-
+
areas = [p.area for p in props]
-
+
fullBorder = [p.label for p in props if p.area == np.max(areas)][0]
-
+
centerRawByRaw = np.array([((np.min(np.where(edges[raw,:])[0])+np.max(np.where(edges[raw,:])[0]))/2,raw)
for raw in range(edges.shape[0])
if len(np.where(edges[raw,:])[0]) != 0 and
(np.max(np.where(edges[raw,:])[0])-np.min(np.where(edges[raw,:])[0])) > 100])
-
+
meanCenter = np.median(centerRawByRaw,axis=0)
-
+
rows = np.where(self.img == fullBorder)[0]
cols = np.where(self.img == fullBorder)[1]
-
+
ya = np.mean(rows[np.where(cols == np.min(cols))])
yb = np.mean(rows[np.where(cols == np.max(cols))])
xb = np.max(cols)
xa = np.min(cols)
-
+
slope = (yb-ya)/(xb-xa)
-
+
self.centerX = (self.centImgY-meanCenter[1])/slope + meanCenter[0]
-
+
offsetSX = (self.centImgX-self.centerX)*self.resolution*10**-3
-
-
+
+
centerXCalculationTime = time.time()-start
self.totalProcessingTime += centerXCalculationTime
-
+
print("Time to calculate sample center X: "+str(centerXCalculationTime))
-
+
return offsetSX
-
-
+
+
def sampleCenterYCalculation(self):
pass
-
+
def localTomoCenterXCalculation(self):
-
+
start = time.time()
-
+
props = measure.regionprops(self.img,self.intImg)
-
+
areas = [p.area for p in props]
-
+
border = [p.centroid for p in props if p.area == np.max(areas) and p.max_intensity > 200]
-
+
if len(border) == 0:
-
+
offsetSX = self.img.shape[1]
-
+
else:
-
+
ret,binImg = cv2.threshold(self.dispImg,0,1,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)
-
+
labImg = measure.label(binImg, neighbors=8, background=0)
labImg += 1
props = measure.regionprops(labImg)
-
+
areas = [p.area for p in props]
-
+
sample = [p.centroid for p in props if p.area == np.max(areas)][0]
-
+
if sample[1] > border[0][1]:
-
+
self.borderDetected = "right"
-
+
else:
self.borderDetected = "left"
-
+
self.centerX = border[0][1]
-
+
offsetSX = (self.centImgX-self.centerX)*self.resolution*10**-3
-
+
centerXCalculationTime = time.time()-start
self.totalProcessingTime += centerXCalculationTime
-
+
print("Time to calculate sample center X: "+str(centerXCalculationTime))
-
+
return offsetSX
def displayResults(self):
-
+
try:
self.centerX
except NameError:
@@ -293,26 +293,26 @@ class OffsetsCalculation:
self.centerY
except NameError:
self.centerY = 0
-
+
print('\n')
print('total processing time: '+str(self.totalProcessingTime))
print('\n')
print('Sample center detected: '+str(self.centerX)+' in X and: '+str(self.centerY)+' in Y')
print('Image center: '+str(self.centImgX)+' in X and: '+str(self.centImgY)+' in Y')
-
+
def displayImage(self):
-
+
edgesDetection = fabio.open('/segfs/tango/tmp/clemence/SampleAlignment/edgesDetected.edf')
-
+
qapp = qt.QApplication([])
plot = Plot2D()
plot.addImage(edgesDetection.data, legend='image')
plot.show()
qapp.exec_()
-
+
if __name__ == '__main__':
-
+
test = OffsetsCalculation(12.57,"/segfs/tango/tmp/clemence/SampleAlignment/","absent","straight")
test.imagesOpening()
test.imageContrastEnhancement()
@@ -323,5 +323,5 @@ if __name__ == '__main__':
#test.displayResults()
#inst = OffsetsCalculation(0,"","","")
#inst.displayImage()
-
-
+
+
diff --git a/SampleAlignment/TomoSampleAlign.py b/SampleAlignment/TomoSampleAlign.py
index c6ef7bd..86cec66 100644
--- a/SampleAlignment/TomoSampleAlign.py
+++ b/SampleAlignment/TomoSampleAlign.py
@@ -43,35 +43,35 @@ class TomoSampleAlign(Device):
"""
__metaclass__ = DeviceMeta
# PROTECTED REGION ID(TomoSampleAlign.class_variable) ENABLED START #
-
+
green_mode = PyTango.GreenMode.Gevent
-
+
#
# Blocking operation to find sample center
#
def alignment_task(self):
try:
self.info_stream("started alignment")
-
+
self.is_error = False
self.is_moving = True
-
+
# alignment code
print ("Alignment start\n")
-
+
#gevent.sleep(3)
-
+
align = OffsetsCalculation(self.attr_Resolution_read,self.attr_ImageDirectory_read,self.attr_StandDetection_read,self.attr_BorderType_read)
align.imagesOpening()
align.imageContrastEnhancement()
align.imageFiltering()
align.edgesDetection()
-
+
if self.attr_AlignX_read:
if self.attr_LocalTomo_read == True:
offsetSX = align.localTomoCenterXCalculation()
self.attr_BorderDetected_read = align.borderDetected
-
+
print(self.attr_BorderDetected_read)
else:
offsetSX = align.sampleCenterXCalculation()
@@ -81,22 +81,22 @@ class TomoSampleAlign(Device):
offsetSY = align.sampleCenterYCalculation()
else:
offsetSY = 0
-
+
align.displayResults()
-
-
+
+
print('Offset detected: '+str(int(offsetSX/(self.attr_Resolution_read*10**-3)))+' in X and: '+str(int(offsetSY/(self.attr_Resolution_read*10**-3)))+' in Y')
print('Relative SY moving of '+str(offsetSX))
print('Relative SZ moving of '+str(offsetSY))
-
+
self.attr_AlignmentOffsets_read = [offsetSX,offsetSY]
-
+
self.is_moving = False
-
+
self.info_stream("\nfinished alignment")
-
-
-
+
+
+
# catch all exceptions, print the traceback to the console and
# add the information to the device status until acknowledgement
except:
@@ -106,10 +106,10 @@ class TomoSampleAlign(Device):
except PyTango.DevFailed as ex:
self.task_error = ex
PyTango.Except.print_exception(ex)
-
+
self.is_error = True
self.is_moving = False
-
+
# PROTECTED REGION END # // TomoSampleAlign.class_variable
# ----------
@@ -183,13 +183,13 @@ class TomoSampleAlign(Device):
Device.init_device(self)
# PROTECTED REGION ID(TomoSampleAlign.init_device) ENABLED START #
# init flags for state and status
-
+
self.is_moving = False
self.is_error = False
-
+
self.running_task = None
self.task_error = None
-
+
self.attr_SampleSizeZ_read = 0.0
self.attr_SampleSizeY_read = 0.0
self.attr_SampleSizeX_read = 0.0
@@ -201,7 +201,7 @@ class TomoSampleAlign(Device):
self.attr_AlignY_read = False
self.attr_AlignmentOffsets_read = [0.0,0.0]
print("done!")
-
+
# PROTECTED REGION END # // TomoSampleAlign.init_device
def always_executed_hook(self):
@@ -416,7 +416,7 @@ class TomoSampleAlign(Device):
_state = PyTango.DevState.MOVING
else:
_state = PyTango.DevState.ON
-
+
self.set_state(_state)
return _state
# PROTECTED REGION END # // TomoSampleAlign.State
@@ -425,7 +425,7 @@ class TomoSampleAlign(Device):
def dev_status(self):
# PROTECTED REGION ID(TomoSampleAlign.Status) ENABLED START #
state = self.dev_state()
-
+
self._status = "The device state is "
if state == PyTango.DevState.FAULT:
self._status += "FAULT"
@@ -444,7 +444,7 @@ class TomoSampleAlign(Device):
self._status += "MOVING"
else:
self._status += "ON"
-
+
self.set_status(self._status)
return self._status
# PROTECTED REGION END # // TomoSampleAlign.Status
@@ -454,12 +454,12 @@ class TomoSampleAlign(Device):
@DebugIt()
def AlignSample(self):
# PROTECTED REGION ID(TomoSampleAlign.AlignSample) ENABLED START #
-
+
self.running_task = gevent.spawn(self.alignment_task)
print("Running started")
self.is_moving = True
-
-
+
+
# PROTECTED REGION END # // TomoSampleAlign.AlignSample
def is_AlignSample_allowed(self):
@@ -474,10 +474,10 @@ class TomoSampleAlign(Device):
def main(args=None, **kwargs):
# PROTECTED REGION ID(TomoSampleAlign.main) ENABLED START #
-
+
# Enable gevents for the server
kwargs.setdefault("green_mode", PyTango.GreenMode.Gevent)
-
+
return run((TomoSampleAlign,), args=args, **kwargs)
# PROTECTED REGION END # // TomoSampleAlign.main
diff --git a/SamplesDS/TomoSample.py b/SamplesDS/TomoSample.py
index 605eec0..c149c1d 100644
--- a/SamplesDS/TomoSample.py
+++ b/SamplesDS/TomoSample.py
@@ -110,7 +110,7 @@ class TomoSample(Device):
def init_device(self):
Device.init_device(self)
# PROTECTED REGION ID(TomoSample.init_device) ENABLED START #
-
+
self.attr_Name_read = "None"
self.attr_Position_read = "None"
self.attr_SizeX_read = 0.0
@@ -120,13 +120,13 @@ class TomoSample(Device):
self.attr_AlignSY_read = 0.0
self.attr_AlignSZ_read = 0.0
self.attr_Aligned_read = False
-
+
#
# Get sample changer position from the device name
dev_name = self.get_name()
dom, fam, member = dev_name.split("/")
self.attr_Position_read = member
-
+
# PROTECTED REGION END # // TomoSample.init_device
def always_executed_hook(self):
@@ -236,12 +236,12 @@ class TomoSample(Device):
@DebugIt()
def dev_state(self):
# PROTECTED REGION ID(TomoSample.State) ENABLED START #
-
+
if self.attr_Name_read == "None":
_state = PyTango.DevState.DISABLE
else:
_state = PyTango.DevState.ON
-
+
self.set_state(_state)
return _state
# PROTECTED REGION END # // TomoSample.State
@@ -251,7 +251,7 @@ class TomoSample(Device):
@DebugIt()
def Reset(self):
# PROTECTED REGION ID(TomoSample.Reset) ENABLED START #
-
+
myself = PyTango.DeviceProxy (self.get_name())
myself.write_attribute_asynch("Name" , "None")
myself.write_attribute_asynch("SizeX" , 0)
@@ -261,7 +261,7 @@ class TomoSample(Device):
myself.write_attribute_asynch("AlignSY" , 0)
myself.write_attribute_asynch("AlignSZ" , 0)
myself.write_attribute_asynch("Aligned" , False)
-
+
# PROTECTED REGION END # // TomoSample.Reset
# ----------
--
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