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GEPARD
GEPARD
Commits
f1fcb2d7
Commit
f1fcb2d7
authored
Dec 02, 2019
by
Josef Brandt
Browse files
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Browse Files
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Email Patches
Plain Diff
Autofocus Option selectable by checkbox in WITecCom
parent
d6102fea
Changes
5
Hide whitespace changes
Inline
Side-by-side
Showing
5 changed files
with
139 additions
and
107 deletions
+139
-107
.gitignore
.gitignore
+6
-0
ramancom/WITecCOM.py
ramancom/WITecCOM.py
+12
-7
ramanscanui.py
ramanscanui.py
+42
-26
sampleview.py
sampleview.py
+4
-3
segmentation.py
segmentation.py
+75
-71
No files found.
.gitignore
View file @
f1fcb2d7
...
...
@@ -18,3 +18,9 @@ external/build/
ramancom/renishawcom.py
ramancom/renishawtesting.py
*.exp
*.lib
*.obj
ramancom/WITecCOM.py
View file @
f1fcb2d7
...
...
@@ -53,7 +53,9 @@ class WITecCOM(RamanBase):
hostname
=
gethostname
()
self
.
IBUCSAccess
=
win32com
.
client
.
DispatchEx
(
self
.
CLSID
,
machine
=
hostname
,
clsctx
=
pythoncom
.
CLSCTX_REMOTE_SERVER
)
self
.
advancedInterface
=
False
self
.
doAutoFocus
=
False
def
connect
(
self
):
if
not
self
.
IBUCSAccess
.
RequestWriteAccess
(
True
):
self
.
connected
=
False
...
...
@@ -167,9 +169,8 @@ class WITecCOM(RamanBase):
try
:
self
.
getAdvancedCOMFeatures
(
IBUCSCore
)
self
.
advancedInterface
=
True
print
(
'using advanced WITec features!'
)
self
.
doAutoFocus
=
False
except
pythoncom
.
com_error
:
print
(
'not using advanced WITec features!'
)
self
.
advancedInterface
=
False
self
.
connected
=
True
...
...
@@ -201,9 +202,9 @@ class WITecCOM(RamanBase):
from
.advancedWITec
import
AdvancedWITecSpectra
except
ModuleNotFoundError
:
from
advancedWITec
import
AdvancedWITecSpectra
self
.
advSpec
=
AdvancedWITecSpectra
()
self
.
ramanParameters
.
append
(
RamanSettingParam
(
'Autofocus'
,
'checkBox'
,
default
=
Tru
e
))
self
.
advSpec
=
AdvancedWITecSpectra
()
if
'Autofocus'
not
in
[
param
.
name
for
param
in
self
.
ramanParameters
]:
self
.
ramanParameters
.
append
(
RamanSettingParam
(
'Autofocus'
,
'checkBox'
,
default
=
Fals
e
))
def
getBrightness
(
self
):
assert
self
.
connected
...
...
@@ -342,7 +343,8 @@ class WITecCOM(RamanBase):
if
not
self
.
advancedInterface
:
self
.
triggerTimeSeriesMeasurement
(
num
)
else
:
self
.
doSpectralAutoFocus
()
if
self
.
doAutoFocus
:
self
.
doSpectralAutoFocus
()
self
.
acquireSilentSpectrum
(
num
)
def
finishMeasurement
(
self
):
...
...
@@ -378,6 +380,9 @@ class WITecCOM(RamanBase):
def
initateSilentSpectrumAcquisition
(
self
,
ramanSettings
):
self
.
advSpec
.
setDatasetPath
(
ramanSettings
[
'path'
])
self
.
doAutoFocus
=
ramanSettings
[
'Autofocus'
]
self
.
advSpec
.
createTmpSpecFolder
()
state
=
self
.
BeamPathState
.
GetValue
()
if
state
==
'Video'
:
...
...
ramanscanui.py
View file @
f1fcb2d7
...
...
@@ -99,33 +99,13 @@ class RamanScanUI(QtWidgets.QWidget):
hbox
=
QtWidgets
.
QHBoxLayout
()
self
.
params
=
[]
for
param
in
self
.
ramanctrl
.
ramanParameters
:
if
param
.
dtype
==
'int'
:
self
.
params
.
append
(
QtWidgets
.
QSpinBox
())
self
.
params
[
-
1
].
setMinimum
(
param
.
minVal
)
self
.
params
[
-
1
].
setMaximum
(
param
.
maxVal
)
self
.
params
[
-
1
].
setValue
(
param
.
value
)
if
param
.
dtype
==
'double'
:
self
.
params
.
append
(
QtWidgets
.
QDoubleSpinBox
())
self
.
params
[
-
1
].
setMinimum
(
param
.
minVal
)
self
.
params
[
-
1
].
setMaximum
(
param
.
maxVal
)
self
.
params
[
-
1
].
setValue
(
param
.
value
)
if
param
.
dtype
==
'combobox'
:
self
.
params
.
append
(
QtWidgets
.
QComboBox
())
self
.
params
[
-
1
].
addItems
([
str
(
i
)
for
i
in
param
.
valList
])
self
.
group2
=
QtWidgets
.
QGroupBox
(
"Raman settings"
,
self
)
grid2
=
QtWidgets
.
QFormLayout
()
for
index
,
param
in
enumerate
(
self
.
params
):
param
.
setMinimumWidth
(
70
)
grid2
.
addRow
(
QtWidgets
.
QLabel
(
self
.
ramanctrl
.
ramanParameters
[
index
].
name
),
param
)
self
.
paramsGroup
=
QtWidgets
.
QGroupBox
(
"Raman settings"
)
self
.
paramsLayout
=
QtWidgets
.
QFormLayout
()
self
.
prun
=
QtWidgets
.
QPushButton
(
"Raman scan"
,
self
)
self
.
prun
.
released
.
connect
(
self
.
run
)
grid2
.
addRow
(
self
.
prun
)
self
.
group2
.
setLayout
(
grid2
)
self
.
paramsGroup
.
setLayout
(
self
.
paramsLayout
)
self
.
updateRamanParameters
(
)
self
.
pexit
=
QtWidgets
.
QPushButton
(
"Cancel"
,
self
)
self
.
pexit
.
released
.
connect
(
self
.
stopScan
)
...
...
@@ -139,7 +119,7 @@ class RamanScanUI(QtWidgets.QWidget):
hbox
.
addStretch
()
hbox
.
addWidget
(
self
.
pexit
)
vbox
.
addWidget
(
self
.
g
roup
2
)
vbox
.
addWidget
(
self
.
paramsG
roup
)
vbox
.
addLayout
(
hbox
)
vbox
.
addWidget
(
self
.
progresstime
)
vbox
.
addWidget
(
self
.
progressbar
)
...
...
@@ -148,6 +128,42 @@ class RamanScanUI(QtWidgets.QWidget):
self
.
setWindowTitle
(
"Raman Scan"
)
self
.
setVisible
(
False
)
def
updateRamanParameters
(
self
):
"""
Update the raman parameters in the layout
:return:
"""
for
index
in
reversed
(
range
(
self
.
paramsLayout
.
count
())):
widget
=
self
.
paramsLayout
.
itemAt
(
index
).
widget
()
self
.
paramsLayout
.
removeWidget
(
widget
)
widget
.
setParent
(
None
)
self
.
params
=
[]
for
param
in
self
.
ramanctrl
.
ramanParameters
:
if
param
.
dtype
==
'int'
:
self
.
params
.
append
(
QtWidgets
.
QSpinBox
())
self
.
params
[
-
1
].
setMinimum
(
param
.
minVal
)
self
.
params
[
-
1
].
setMaximum
(
param
.
maxVal
)
self
.
params
[
-
1
].
setValue
(
param
.
value
)
if
param
.
dtype
==
'double'
:
self
.
params
.
append
(
QtWidgets
.
QDoubleSpinBox
())
self
.
params
[
-
1
].
setMinimum
(
param
.
minVal
)
self
.
params
[
-
1
].
setMaximum
(
param
.
maxVal
)
self
.
params
[
-
1
].
setValue
(
param
.
value
)
if
param
.
dtype
==
'combobox'
:
self
.
params
.
append
(
QtWidgets
.
QComboBox
())
self
.
params
[
-
1
].
addItems
([
str
(
i
)
for
i
in
param
.
valList
])
if
param
.
dtype
==
'checkBox'
:
self
.
params
.
append
(
QtWidgets
.
QCheckBox
())
self
.
params
[
-
1
].
setChecked
(
param
.
value
)
for
index
,
param
in
enumerate
(
self
.
params
):
param
.
setMinimumWidth
(
70
)
self
.
paramsLayout
.
addRow
(
QtWidgets
.
QLabel
(
self
.
ramanctrl
.
ramanParameters
[
index
].
name
),
param
)
self
.
paramsLayout
.
addRow
(
self
.
prun
)
self
.
paramsGroup
.
setLayout
(
self
.
paramsLayout
)
def
makeGetFnameLambda
(
self
,
msg
,
path
,
fileType
,
btn
):
return
lambda
:
self
.
getFName
(
msg
,
path
,
fileType
,
btn
)
...
...
@@ -247,7 +263,7 @@ class RamanScanUI(QtWidgets.QWidget):
else
:
self
.
view
.
highLightRamanIndex
(
0
)
self
.
view
.
blockUI
()
self
.
g
roup
2
.
setEnabled
(
False
)
self
.
paramsG
roup
.
setEnabled
(
False
)
self
.
progresstime
.
setEnabled
(
True
)
self
.
progressbar
.
setEnabled
(
True
)
self
.
progressbar
.
setRange
(
0
,
len
(
scanpoints
))
...
...
sampleview.py
View file @
f1fcb2d7
...
...
@@ -220,6 +220,7 @@ class SampleView(QtWidgets.QGraphicsView):
elif
mode
==
"RamanScan"
:
self
.
removeSeedPointMarkers
()
self
.
ramanwidget
.
resetDataset
(
self
.
dataset
)
self
.
ramanwidget
.
updateRamanParameters
()
self
.
ramanwidget
.
setVisible
(
True
)
#show legend:
...
...
@@ -350,9 +351,9 @@ class SampleView(QtWidgets.QGraphicsView):
p0
=
self
.
mapToScene
(
event
.
pos
())
self
.
moveStageToPosition
(
p0
)
#
elif self.mode=="ParticleDetection":
#
p0 = self.mapToScene(event.pos())
#
self.detectionwidget.setImageCenter([p0.x(), p0.y()])
elif
self
.
mode
==
"ParticleDetection"
:
p0
=
self
.
mapToScene
(
event
.
pos
())
self
.
detectionwidget
.
setImageCenter
([
p0
.
x
(),
p0
.
y
()])
else
:
p0
=
self
.
mapToScene
(
event
.
pos
())
...
...
segmentation.py
View file @
f1fcb2d7
...
...
@@ -110,7 +110,7 @@ class Segmentation(object):
Parameter
(
"maxholebrightness"
,
float
,
self
.
detectParams
[
'maxholebrightness'
],
0
,
1
,
2
,
0.02
,
helptext
=
"Close holes brighter than.."
,
show
=
True
),
Parameter
(
"minparticlearea"
,
int
,
self
.
detectParams
[
'minparticlearea'
],
1
,
1000
,
0
,
50
,
helptext
=
"Min. particle pixel area"
,
show
=
False
),
Parameter
(
"enableMaxArea"
,
np
.
bool
,
self
.
detectParams
[
'enableMaxArea'
],
helptext
=
"enable filtering for maximal pixel area"
,
show
=
False
,
linkedParameter
=
'maxparticlearea'
),
Parameter
(
"maxparticlearea"
,
int
,
self
.
detectParams
[
'maxparticlearea'
],
10
,
1E9
,
0
,
50
,
helptext
=
"Max. particle pixel area"
,
show
=
Tru
e
),
Parameter
(
"maxparticlearea"
,
int
,
self
.
detectParams
[
'maxparticlearea'
],
10
,
1E9
,
0
,
50
,
helptext
=
"Max. particle pixel area"
,
show
=
Fals
e
),
Parameter
(
"minparticledistance"
,
int
,
self
.
detectParams
[
'minparticledistance'
],
5
,
1000
,
0
,
5
,
helptext
=
"Min. distance between particles"
,
show
=
False
),
Parameter
(
"measurefrac"
,
float
,
self
.
detectParams
[
'measurefrac'
],
0
,
1
,
2
,
stepsize
=
0.05
,
helptext
=
"measure fraction of particles"
,
show
=
False
),
Parameter
(
"closeBackground"
,
np
.
bool
,
self
.
detectParams
[
'closeBackground'
],
helptext
=
"close holes in sure background"
,
show
=
False
),
...
...
@@ -253,83 +253,87 @@ class Segmentation(object):
for
label
in
range
(
1
,
n
):
area
=
stats
[
label
,
cv2
.
CC_STAT_AREA
]
if
self
.
minparticlearea
<
area
<
maxArea
:
print
(
f
'processing
{
label
}
of
{
n
}
compontents'
)
up
=
stats
[
label
,
cv2
.
CC_STAT_TOP
]
left
=
stats
[
label
,
cv2
.
CC_STAT_LEFT
]
width
=
stats
[
label
,
cv2
.
CC_STAT_WIDTH
]
height
=
stats
[
label
,
cv2
.
CC_STAT_HEIGHT
]
subthresh
=
np
.
uint8
(
255
*
(
labels
[
up
:(
up
+
height
),
left
:(
left
+
width
)]
==
label
))
subdist
=
cv2
.
distanceTransform
(
subthresh
,
cv2
.
DIST_L2
,
3
)
sure_fg
=
self
.
getSureForeground
(
subthresh
,
subdist
,
self
.
minparticledistance
)
sure_bg
=
cv2
.
dilate
(
subthresh
,
np
.
ones
((
5
,
5
)),
iterations
=
1
)
if
self
.
closeBackground
:
sure_bg
=
self
.
closeHoles
(
sure_bg
)
# modify sure_fg and sure_bg with seedpoints and deletepoints
for
p
in
np
.
int32
(
seedpoints
):
cv2
.
circle
(
sure_fg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
1
,
-
1
)
cv2
.
circle
(
sure_bg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
1
,
-
1
)
for
p
in
np
.
int32
(
deletepoints
):
cv2
.
circle
(
sure_fg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
0
,
-
1
)
cv2
.
circle
(
sure_bg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
0
,
-
1
)
if
self
.
cancelcomputation
:
return
None
,
None
if
return_step
==
"sure_fg"
:
preview_surefg
=
self
.
addToPreviewImage
(
sure_fg
,
up
,
left
,
preview_surefg
)
preview_surebg
=
self
.
addToPreviewImage
(
sure_bg
,
up
,
left
,
preview_surebg
)
continue
unknown
=
cv2
.
subtract
(
sure_bg
,
sure_fg
)
ret
,
markers
=
cv2
.
connectedComponents
(
sure_fg
)
markers
=
markers
+
1
markers
[
unknown
==
255
]
=
0
markers
=
ndi
.
label
(
sure_fg
)[
0
]
markers
=
watershed
(
-
subdist
,
markers
,
mask
=
sure_bg
,
compactness
=
self
.
compactness
,
watershed_line
=
True
)
#labels = 0 for background, 1... for particles
if
self
.
cancelcomputation
:
return
None
,
None
if
return_step
==
"watershed"
:
previewImage
=
self
.
addToPreviewImage
(
markers
,
up
,
left
,
previewImage
)
continue
if
cv2
.
__version__
>
'3.5'
:
contours
,
hierarchy
=
cv2
.
findContours
(
markers
,
cv2
.
RETR_CCOMP
,
cv2
.
CHAIN_APPROX_NONE
)
# if width > 25000 or height > 25000:
if
False
:
print
(
f
'skipping
{
label
}
of
{
n
}
compontents, too large:
{
width
}
x
{
height
}
pixel!!!'
)
else
:
temp
,
contours
,
hierarchy
=
cv2
.
findContours
(
markers
,
cv2
.
RETR_CCOMP
,
cv2
.
CHAIN_APPROX_NONE
)
if
self
.
cancelcomputation
:
return
None
,
None
print
(
f
'processing
{
label
}
of
{
n
}
compontents,
{
width
}
x
{
height
}
pixel'
)
subthresh
=
np
.
uint8
(
255
*
(
labels
[
up
:(
up
+
height
),
left
:(
left
+
width
)]
==
label
))
subdist
=
cv2
.
distanceTransform
(
subthresh
,
cv2
.
DIST_L2
,
3
)
tmpcontours
=
[
contours
[
i
]
for
i
in
range
(
len
(
contours
))
if
hierarchy
[
0
,
i
,
3
]
<
0
]
for
cnt
in
tmpcontours
:
if
cv2
.
contourArea
(
cnt
)
>=
self
.
minparticlearea
:
label
=
markers
[
cnt
[
0
,
0
,
1
],
cnt
[
0
,
0
,
0
]]
if
label
==
0
:
continue
x0
,
x1
=
cnt
[:,
0
,
0
].
min
(),
cnt
[:,
0
,
0
].
max
()
y0
,
y1
=
cnt
[:,
0
,
1
].
min
(),
cnt
[:,
0
,
1
].
max
()
subimg
=
(
markers
[
y0
:
y1
+
1
,
x0
:
x1
+
1
]).
copy
()
subimg
[
subimg
!=
label
]
=
0
y
,
x
=
self
.
getMeasurementPoints
(
subimg
)
for
i
in
range
(
len
(
cnt
)):
cnt
[
i
][
0
][
0
]
+=
left
cnt
[
i
][
0
][
1
]
+=
up
finalcontours
.
append
(
cnt
)
measurementPoints
[
particleIndex
]
=
[]
sure_fg
=
self
.
getSureForeground
(
subthresh
,
subdist
,
self
.
minparticledistance
)
sure_bg
=
cv2
.
dilate
(
subthresh
,
np
.
ones
((
5
,
5
)),
iterations
=
1
)
if
self
.
closeBackground
:
sure_bg
=
self
.
closeHoles
(
sure_bg
)
# modify sure_fg and sure_bg with seedpoints and deletepoints
for
p
in
np
.
int32
(
seedpoints
):
cv2
.
circle
(
sure_fg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
1
,
-
1
)
cv2
.
circle
(
sure_bg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
1
,
-
1
)
for
p
in
np
.
int32
(
deletepoints
):
cv2
.
circle
(
sure_fg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
0
,
-
1
)
cv2
.
circle
(
sure_bg
,
tuple
([
p
[
0
]
-
left
,
p
[
1
]
-
up
]),
int
(
p
[
2
]),
0
,
-
1
)
if
self
.
cancelcomputation
:
return
None
,
None
if
return_step
==
"sure_fg"
:
preview_surefg
=
self
.
addToPreviewImage
(
sure_fg
,
up
,
left
,
preview_surefg
)
preview_surebg
=
self
.
addToPreviewImage
(
sure_bg
,
up
,
left
,
preview_surebg
)
continue
unknown
=
cv2
.
subtract
(
sure_bg
,
sure_fg
)
ret
,
markers
=
cv2
.
connectedComponents
(
sure_fg
)
markers
=
markers
+
1
markers
[
unknown
==
255
]
=
0
markers
=
ndi
.
label
(
sure_fg
)[
0
]
markers
=
watershed
(
-
subdist
,
markers
,
mask
=
sure_bg
,
compactness
=
self
.
compactness
,
watershed_line
=
True
)
#labels = 0 for background, 1... for particles
if
self
.
cancelcomputation
:
return
None
,
None
if
return_step
==
"watershed"
:
previewImage
=
self
.
addToPreviewImage
(
markers
,
up
,
left
,
previewImage
)
continue
if
cv2
.
__version__
>
'3.5'
:
contours
,
hierarchy
=
cv2
.
findContours
(
markers
,
cv2
.
RETR_CCOMP
,
cv2
.
CHAIN_APPROX_NONE
)
else
:
temp
,
contours
,
hierarchy
=
cv2
.
findContours
(
markers
,
cv2
.
RETR_CCOMP
,
cv2
.
CHAIN_APPROX_NONE
)
if
self
.
cancelcomputation
:
return
None
,
None
for
index
in
range
(
0
,
len
(
x
)):
newMeasPoint
=
MeasurementPoint
(
particleIndex
,
x
[
index
]
+
x0
+
left
,
y
[
index
]
+
y0
+
up
)
measurementPoints
[
particleIndex
].
append
(
newMeasPoint
)
particleIndex
+=
1
tmpcontours
=
[
contours
[
i
]
for
i
in
range
(
len
(
contours
))
if
hierarchy
[
0
,
i
,
3
]
<
0
]
for
cnt
in
tmpcontours
:
if
cv2
.
contourArea
(
cnt
)
>=
self
.
minparticlearea
:
label
=
markers
[
cnt
[
0
,
0
,
1
],
cnt
[
0
,
0
,
0
]]
if
label
==
0
:
continue
x0
,
x1
=
cnt
[:,
0
,
0
].
min
(),
cnt
[:,
0
,
0
].
max
()
y0
,
y1
=
cnt
[:,
0
,
1
].
min
(),
cnt
[:,
0
,
1
].
max
()
subimg
=
(
markers
[
y0
:
y1
+
1
,
x0
:
x1
+
1
]).
copy
()
subimg
[
subimg
!=
label
]
=
0
y
,
x
=
self
.
getMeasurementPoints
(
subimg
)
for
i
in
range
(
len
(
cnt
)):
cnt
[
i
][
0
][
0
]
+=
left
cnt
[
i
][
0
][
1
]
+=
up
finalcontours
.
append
(
cnt
)
measurementPoints
[
particleIndex
]
=
[]
for
index
in
range
(
0
,
len
(
x
)):
newMeasPoint
=
MeasurementPoint
(
particleIndex
,
x
[
index
]
+
x0
+
left
,
y
[
index
]
+
y0
+
up
)
measurementPoints
[
particleIndex
].
append
(
newMeasPoint
)
particleIndex
+=
1
if
return_step
==
'sure_fg'
:
img
=
np
.
zeros_like
(
preview_surefg
)
...
...
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