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GEPARD
GEPARD
Commits
c90f7b26
Commit
c90f7b26
authored
Aug 22, 2019
by
JosefBrandt
Browse files
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Plain Diff
Several Bugfixes
parent
2026524b
Changes
6
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Inline
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Showing
6 changed files
with
45 additions
and
20 deletions
+45
-20
analysis/analysisplots.py
analysis/analysisplots.py
+1
-1
analysis/particleCharacterization.py
analysis/particleCharacterization.py
+13
-1
analysis/particleEditor.py
analysis/particleEditor.py
+8
-2
gepard.py
gepard.py
+2
-2
legacyConvert.py
legacyConvert.py
+5
-0
sampleview.py
sampleview.py
+16
-14
No files found.
analysis/analysisplots.py
View file @
c90f7b26
...
...
@@ -113,7 +113,7 @@ class SpectraPlot(QtWidgets.QGroupBox):
layout
=
QtWidgets
.
QHBoxLayout
()
self
.
canvas
=
FigureCanvas
(
Figure
())
self
.
spec_axis
=
self
.
canvas
.
figure
.
subplots
()
self
.
reference_ax
=
self
.
spec_axis
.
twinx
()
self
.
reference_ax
is
=
self
.
spec_axis
.
twinx
()
self
.
canvas
.
figure
.
subplots_adjust
(
left
=
0.1
,
top
=
0.93
,
bottom
=
0.15
,
right
=
0.9
)
specNavigation
=
NavigationToolbar
(
self
.
canvas
,
self
)
specNavigation
.
setOrientation
(
QtCore
.
Qt
.
Vertical
)
...
...
analysis/particleCharacterization.py
View file @
c90f7b26
...
...
@@ -60,12 +60,24 @@ def getParticleStatsWithPixelScale(cnt, fullimage, dataset):
newStats
.
height
=
getParticleHeight
(
cnt
,
dataset
)
newStats
.
shape
=
getParticleShape
(
cnt
,
newStats
.
height
)
if
newStats
.
shape
==
'fibre'
:
newStats
.
longSize
,
newStats
.
shortSize
=
getFibreDimension
(
cnt
)
newStats
.
longSize
*=
pixelscale
newStats
.
shortSize
*=
pixelscale
partImg
=
getParticleImageFromFullimage
(
cnt
,
fullimage
)
newStats
.
color
=
getParticleColor
(
partImg
)
return
newStats
def
getFibreDimension
(
contour
):
longSize
=
cv2
.
arcLength
(
contour
,
True
)
/
2
img
=
contoursToImg
([
contour
])[
0
]
dist
=
cv2
.
distanceTransform
(
img
,
cv2
.
DIST_L2
,
3
)
maxThickness
=
np
.
max
(
dist
)
*
2
return
longSize
,
maxThickness
def
getParticleColor
(
imgRGB
,
colorClassifier
=
None
):
img
=
cv2
.
cvtColor
(
imgRGB
,
cv2
.
COLOR_RGB2HSV_FULL
)
meanHSV
=
cv2
.
mean
(
img
)
...
...
analysis/particleEditor.py
View file @
c90f7b26
...
...
@@ -171,7 +171,7 @@ class ParticleEditor(QtCore.QObject):
'Particle contours are not connected.
\n
That is currently not supported!'
)
return
self
.
mergeParticlesInParticleContainerAndSampleView
(
contourIndices
,
newContour
,
newAssignment
)
self
.
mergeParticlesInParticleContainerAndSampleView
(
contourIndices
,
newContour
,
newAssignment
)
@
QtCore
.
pyqtSlot
(
list
,
str
)
def
reassignParticles
(
self
,
contourindices
,
newAssignment
):
...
...
@@ -179,13 +179,15 @@ class ParticleEditor(QtCore.QObject):
print
(
f
'reassigning indices
{
contourindices
}
into
{
newAssignment
}
'
)
for
partIndex
in
contourindices
:
self
.
particleContainer
.
reassignParticleToAssignment
(
partIndex
,
newAssignment
)
self
.
viewparent
.
updateParticleInfoBox
(
partIndex
)
self
.
particleAssignmentChanged
.
emit
()
@
QtCore
.
pyqtSlot
(
list
,
str
)
def
paintParticles
(
self
,
contourIndices
,
newAssignment
):
print
(
f
'painting indices
{
contourIndices
}
into
{
newAssignment
}
'
)
self
.
createSafetyBackup
()
self
.
viewparent
.
removeParticleInfoBox
()
self
.
storedIndices
=
contourIndices
self
.
storedAssignmend
=
newAssignment
...
...
@@ -208,6 +210,7 @@ class ParticleEditor(QtCore.QObject):
except
NotConnectedContoursError
:
QtWidgets
.
QMessageBox
.
critical
(
self
.
viewparent
,
'ERROR!'
,
'Particle contours are not connected.
\n
That is currently not supported!'
)
self
.
viewparent
.
updateParticleInfoBox
(
self
.
storedIndices
[
-
1
])
self
.
storedIndices
=
[]
self
.
storedAssignmend
=
None
self
.
destroyParticlePainter
()
...
...
@@ -238,6 +241,7 @@ class ParticleEditor(QtCore.QObject):
self
.
viewparent
.
resetContourIndices
()
self
.
particleContainer
.
resetParticleIndices
()
self
.
viewparent
.
updateParticleInfoBox
(
self
.
particleContainer
.
getNumberOfParticles
()
-
1
)
self
.
particleAssignmentChanged
.
emit
()
@
QtCore
.
pyqtSlot
(
list
,
str
)
...
...
@@ -245,12 +249,14 @@ class ParticleEditor(QtCore.QObject):
print
(
f
'changing color of particles
{
contourIndices
}
into
{
newColor
}
'
)
for
partIndex
in
contourIndices
:
self
.
particleContainer
.
changeParticleColor
(
partIndex
,
newColor
)
self
.
viewparent
.
updateParticleInfoBox
(
partIndex
)
@
QtCore
.
pyqtSlot
(
list
,
str
)
def
changeParticleShapes
(
self
,
contourIndices
,
newShape
):
print
(
f
'changing shape of particles
{
contourIndices
}
into
{
newShape
}
'
)
for
partIndex
in
contourIndices
:
self
.
particleContainer
.
changeParticleShape
(
partIndex
,
newShape
)
self
.
viewparent
.
updateParticleInfoBox
(
partIndex
)
@
QtCore
.
pyqtSlot
(
list
)
def
deleteParticles
(
self
,
contourIndices
):
...
...
gepard.py
View file @
c90f7b26
...
...
@@ -352,8 +352,8 @@ if __name__ == '__main__':
logname
=
os
.
path
.
join
(
logpath
,
'logfile.txt'
)
fp
=
open
(
logname
,
"a"
)
#
sys.stderr = fp
#
sys.stdout = fp
sys
.
stderr
=
fp
sys
.
stdout
=
fp
print
(
"starting GEPARD at: "
+
strftime
(
"%d %b %Y %H:%M:%S"
,
localtime
()),
flush
=
True
)
gepard
=
GEPARDMainWindow
(
logpath
)
...
...
legacyConvert.py
View file @
c90f7b26
...
...
@@ -191,6 +191,11 @@ def updateParticleStats(dset):
except
InvalidParticleError
:
markForDeletion
(
particle
)
if
particle
.
shape
==
'fibre'
:
particle
.
longSize
,
particle
.
shortSize
=
pc
.
getFibreDimension
(
particle
.
contour
)
particle
.
longSize
*=
dset
.
getPixelScale
()
particle
.
shortSize
*=
dset
.
getPixelScale
()
print
(
f
'deleting
{
len
(
deleteIndices
)
}
particles'
)
for
index
in
sorted
(
deleteIndices
,
reverse
=
True
):
dset
.
particleContainer
.
removeParticle
(
index
)
...
...
sampleview.py
View file @
c90f7b26
...
...
@@ -129,7 +129,7 @@ class SampleView(QtWidgets.QGraphicsView):
def
closeEvent
(
self
,
event
):
reply
=
QtWidgets
.
QMessageBox
.
question
(
self
,
'Message'
,
"
Are you sure
to quit?"
,
QtWidgets
.
QMessageBox
.
Yes
|
"
Do you really want
to quit?"
,
QtWidgets
.
QMessageBox
.
Yes
|
QtWidgets
.
QMessageBox
.
No
,
QtWidgets
.
QMessageBox
.
No
)
if
reply
==
QtWidgets
.
QMessageBox
.
Yes
:
...
...
@@ -394,12 +394,6 @@ class SampleView(QtWidgets.QGraphicsView):
cnt
.
update
()
self
.
selectedParticleIndices
.
remove
(
cnt
.
particleIndex
)
def
updateParticleInfoBox
(
index
):
if
self
.
particleInfoBox
is
not
None
:
self
.
scene
().
removeItem
(
self
.
particleInfoBox
)
self
.
particleInfoBox
=
ParticleInfo
(
self
.
dataset
.
particleContainer
.
getParticleOfIndex
(
index
))
self
.
scene
().
addItem
(
self
.
particleInfoBox
)
p
=
self
.
mapToScene
(
event
.
pos
())
p
=
QtCore
.
QPointF
(
p
.
x
(),
p
.
y
())
...
...
@@ -422,10 +416,9 @@ class SampleView(QtWidgets.QGraphicsView):
self
.
selectedParticleIndices
.
remove
(
cnt
.
particleIndex
)
if
len
(
self
.
selectedParticleIndices
)
>
0
:
updateParticleInfoBox
(
self
.
selectedParticleIndices
[
-
1
])
self
.
updateParticleInfoBox
(
self
.
selectedParticleIndices
[
-
1
])
else
:
self
.
scene
().
removeItem
(
self
.
particleInfoBox
)
self
.
particleInfoBox
=
None
self
.
removeParticleInfoBox
()
self
.
update
()
...
...
@@ -614,13 +607,22 @@ class SampleView(QtWidgets.QGraphicsView):
self
.
contourItems
[
index
].
isSelected
=
True
self
.
selectedParticleIndices
=
[
index
]
self
.
updateParticleInfoBox
(
index
)
self
.
update
()
def
updateParticleInfoBox
(
self
,
particleIndex
):
self
.
removeParticleInfoBox
()
self
.
addParticleInfoBox
(
particleIndex
)
def
removeParticleInfoBox
(
self
):
if
self
.
particleInfoBox
is
not
None
:
self
.
scene
().
removeItem
(
self
.
particleInfoBox
)
self
.
particleInfoBox
=
ParticleInfo
(
self
.
dataset
.
particleContainer
.
getParticleOfIndex
(
index
))
self
.
particleInfoBox
=
None
def
addParticleInfoBox
(
self
,
particleIndex
):
self
.
particleInfoBox
=
ParticleInfo
(
self
.
dataset
.
particleContainer
.
getParticleOfIndex
(
particleIndex
))
self
.
scene
().
addItem
(
self
.
particleInfoBox
)
self
.
update
()
def
centerOnRamanIndex
(
self
,
index
,
centerOn
=
True
,
highlightIndex
=
True
):
if
centerOn
:
for
scanItem
in
self
.
ramanscanitems
:
...
...
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