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GEPARD
GEPARD
Commits
8e7707c0
Commit
8e7707c0
authored
Jul 22, 2019
by
JosefBrandt
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Small Bugfixes / Optimizations
parent
3ad72d39
Changes
9
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9 changed files
with
23 additions
and
22 deletions
+23
-22
.gitignore
.gitignore
+4
-0
analysis/analysisview.py
analysis/analysisview.py
+4
-5
analysis/particleContainer.py
analysis/particleContainer.py
+3
-0
analysis/particlePainter.py
analysis/particlePainter.py
+1
-1
dataset.py
dataset.py
+6
-2
detectionview.py
detectionview.py
+0
-1
gepard.py
gepard.py
+2
-2
ramanscanui.py
ramanscanui.py
+0
-1
sampleview.py
sampleview.py
+3
-10
No files found.
.gitignore
View file @
8e7707c0
...
...
@@ -6,3 +6,7 @@ gepard\.cfg
analysis/database_config\.txt
*.so
*.c
external/build/
analysis/analysisview.py
View file @
8e7707c0
...
...
@@ -111,8 +111,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
self
.
specNumberSelector
=
QtWidgets
.
QSpinBox
()
self
.
specNumberSelector
.
setMinimumWidth
(
100
)
self
.
specNumberSelector
.
setMinimum
(
1
)
num
Particles
=
self
.
particleContainer
.
getNumberOf
Particle
s
()
self
.
specNumberSelector
.
setMaximum
(
num
Particles
)
num
Spectra
=
self
.
particleContainer
.
getNumberOf
Measurement
s
()
self
.
specNumberSelector
.
setMaximum
(
num
Spectra
)
self
.
jumpToSpecBtn
=
QtWidgets
.
QPushButton
(
'Jump To Spectrum of Number:'
)
self
.
jumpToSpecBtn
.
released
.
connect
(
self
.
jumpToIndicatedSpectrum
)
...
...
@@ -387,8 +387,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
self
.
typeSelectorCombo
.
addItems
(
uniquePolymers
)
self
.
typeSelectorCombo
.
currentIndexChanged
.
connect
(
self
.
setTypeSelector
)
num
Particles
=
self
.
particleContainer
.
getNumberOf
Particle
s
()
self
.
specNumberSelector
.
setMaximum
(
num
Particles
)
num
Spectra
=
self
.
particleContainer
.
getNumberOf
Measurement
s
()
self
.
specNumberSelector
.
setMaximum
(
num
Spectra
)
def
initializeSpecPlot
(
self
):
self
.
specPlot
.
loadSpectraAndInitializeSpecPlot
()
...
...
@@ -531,7 +531,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
self
.
particleSelector
.
setValue
(
partIndices
.
index
(
particleIndex
)
+
1
)
specIndices
=
self
.
particleContainer
.
getSpectraIndicesOfParticle
(
self
.
currentParticleIndex
)
self
.
spectrumSelector
.
setValue
(
1
)
self
.
spectrumSelector
.
setMaximum
(
len
(
specIndices
))
...
...
analysis/particleContainer.py
View file @
8e7707c0
...
...
@@ -176,6 +176,9 @@ class ParticleContainer(object):
def
getNumberOfParticles
(
self
):
return
len
(
self
.
particles
)
def
getNumberOfMeasurements
(
self
):
return
len
(
self
.
measurements
)
def
getParticleContours
(
self
):
contours
=
[
part
.
contour
for
part
in
self
.
particles
]
return
contours
...
...
analysis/particlePainter.py
View file @
8e7707c0
...
...
@@ -166,7 +166,7 @@ class ParticlePainter(QtWidgets.QGraphicsItem):
painter
.
drawEllipse
(
p
[
0
]
-
p
[
2
],
p
[
1
]
-
p
[
2
],
2
*
p
[
2
],
2
*
p
[
2
])
if
self
.
pixmap
is
not
None
:
painter
.
setOpacity
(
0.
6
)
painter
.
setOpacity
(
0.
4
)
painter
.
drawPixmap
(
self
.
topLeft
[
1
],
self
.
topLeft
[
0
],
self
.
pixmap
)
...
...
dataset.py
View file @
8e7707c0
...
...
@@ -252,6 +252,9 @@ class DataSet(object):
self
.
particleContainer
.
clearMeasurements
()
if
self
.
particles2spectra
is
None
:
self
.
particles2spectra
=
[[
int
(
np
.
where
(
self
.
ramanscansortindex
==
i
)[
0
])]
for
i
in
range
(
len
(
self
.
ramanscansortindex
))]
if
len
(
self
.
particlestats
)
>
0
:
#i.e., particle detection was completed and particle data is there
self
.
particleDetectionDone
=
True
for
particleIndex
,
listOfScanIndices
in
enumerate
(
self
.
particles2spectra
):
...
...
@@ -259,11 +262,12 @@ class DataSet(object):
curParticle
.
measurements
=
[]
for
scanIndex
in
listOfScanIndices
:
indexOfNewMeas
=
self
.
particleContainer
.
addEmptyMeasurement
()
x
,
y
=
self
.
ramanpoints
[
indexOfNewMeas
][
0
],
self
.
ramanpoints
[
indexOfNewMeas
][
1
]
indexOfMeasInRamanPoints
=
self
.
ramanscansortindex
[
scanIndex
]
x
,
y
=
self
.
ramanpoints
[
indexOfMeasInRamanPoints
][
0
],
self
.
ramanpoints
[
indexOfMeasInRamanPoints
][
1
]
self
.
particleContainer
.
setMeasurementPixelCoords
(
indexOfNewMeas
,
x
,
y
)
self
.
particleContainer
.
setMeasurementScanIndex
(
indexOfNewMeas
,
scanIndex
)
curParticle
.
addMeasurement
(
self
.
particleContainer
.
measurements
[
indexOfNewMeas
])
for
particle
in
self
.
particleContainer
.
particles
:
for
meas
in
particle
.
measurements
:
specIndex
=
meas
.
getScanIndex
()
...
...
detectionview.py
View file @
8e7707c0
...
...
@@ -672,7 +672,6 @@ class ParticleDetectionView(QtWidgets.QWidget):
particleContainer
.
setMeasurementPixelCoords
(
indexOfNewMeas
,
point
.
x
,
point
.
y
)
curParticle
.
addMeasurement
(
particleContainer
.
measurements
[
indexOfNewMeas
])
self
.
dataset
.
ramanpoints
=
measurementPoints
self
.
dataset
.
particleDetectionDone
=
True
self
.
dataset
.
mode
=
"prepareraman"
self
.
dataset
.
save
()
...
...
gepard.py
View file @
8e7707c0
...
...
@@ -329,8 +329,8 @@ 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
)
...
...
ramanscanui.py
View file @
8e7707c0
...
...
@@ -234,7 +234,6 @@ class RamanScanUI(QtWidgets.QWidget):
for
measIndex
,
ramanScanIndex
in
enumerate
(
cmin
):
self
.
dataset
.
particleContainer
.
setMeasurementScanIndex
(
measIndex
,
ramanScanIndex
)
self
.
dataset
.
ramanscansortindex
=
cmin
self
.
view
.
saveDataSet
()
self
.
view
.
prepareAnalysis
()
self
.
view
.
scaleImage
(
2.0
)
...
...
sampleview.py
View file @
8e7707c0
...
...
@@ -555,18 +555,11 @@ class SampleView(QtWidgets.QGraphicsView):
def
prepareAnalysis
(
self
):
self
.
clearItems
()
if
self
.
dataset
.
particleDetectionDone
:
data
=
[]
for
i
in
self
.
dataset
.
ramanscansortindex
:
data
.
append
(
list
(
self
.
dataset
.
ramanpoints
[
i
]))
for
i
in
range
(
len
(
data
)):
item
=
RamanScanIndicator
(
self
,
i
+
1
,
20
,
(
data
[
i
][
0
],
data
[
i
][
1
]))
for
meas
in
self
.
dataset
.
particleContainer
.
measurements
:
number
=
meas
.
ramanScanIndex
+
1
item
=
RamanScanIndicator
(
self
,
number
,
20
,
(
meas
.
pixelcoord_x
,
meas
.
pixelcoord_y
))
self
.
scene
().
addItem
(
item
)
self
.
ramanscanitems
.
append
(
item
)
# for index, meas in enumerate(self.dataset.particleContainer.measurements):
# number = meas.ramanScanIndex+1
# item = RamanScanIndicator(self, number, 20, (meas.pixelcoord_x, meas.pixelcoord_y))
# self.scene().addItem(item)
# self.ramanscanitems.append(item)
def
resetParticleContours
(
self
):
t0
=
time
.
time
()
...
...
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