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Josef Brandt
Subsampling
Commits
6d4cec73
Commit
6d4cec73
authored
Mar 30, 2020
by
Josef Brandt
Browse files
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Plain Diff
Timing-Decorator, filter Rotation
parent
5a65802d
Changes
9
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Showing
9 changed files
with
172 additions
and
12 deletions
+172
-12
chemometricMethods.py
chemometricMethods.py
+0
-1
cythonModules/rotateContour.pyx
cythonModules/rotateContour.pyx
+32
-0
cythonModules/setup_cython.py
cythonModules/setup_cython.py
+18
-0
evaluation.py
evaluation.py
+0
-1
gui/filterView.py
gui/filterView.py
+18
-1
gui/mainView.py
gui/mainView.py
+16
-1
gui/measureModes.py
gui/measureModes.py
+4
-3
helpers.py
helpers.py
+23
-5
tests/test_cython.py
tests/test_cython.py
+61
-0
No files found.
chemometricMethods.py
View file @
6d4cec73
...
...
@@ -149,7 +149,6 @@ class ChemometricSubsampling(SubsamplingMethod):
numAmpPoints
=
numClusteredPoints
+
numNoisePoints
*
noiseAmpFactor
fractionPerCluster
=
np
.
clip
(
numPointsToSelect
/
numAmpPoints
,
0.0
,
1.0
)
print
(
'fractionPerCluster, self.fraction'
,
fractionPerCluster
,
self
.
fraction
)
tooFewPoints
=
numPointsToSelect
<
len
(
individualLabels
)
...
...
cythonModules/rotateContour.pyx
0 → 100644
View file @
6d4cec73
import
numpy
as
np
cimport
numpy
as
np
cimport
cython
DTYPE
=
np
.
float
ctypedef
np
.
float_t
DTYPE_t
ctypedef
np
.
int32_t
INT32_t
def
rotate_contour_around_point
(
np
.
ndarray
[
DTYPE_t
,
ndim
=
3
]
contour
,
np
.
ndarray
[
DTYPE_t
,
ndim
=
1
]
refPoint
,
np
.
float
angleDegree
):
# def rotate_contour_around_point(contour: np.ndarray, refPoint: tuple, angleDegree: float) -> np.ndarray:
"""
Rotates a point around another one...
:param contour: Array of points to be rotated, [:, 0, 0] = x, [:, 0, 1] = y
:param refPoint: The referemce point around which the first point is rotated, tuple of x and y
:param angleDegree: The angle in degree to rotate (counter-clockwise)
:return: Array of the rotated point, [:, 0, 0] = x, [:, 0, 1] = y
"""
cdef
int
i
cdef
double
theta
,
sin
,
cos
,
x
,
y
cdef
np
.
ndarray
[
DTYPE_t
,
ndim
=
3
]
newContour
theta
=
np
.
deg2rad
(
angleDegree
)
sin
=
np
.
sin
(
theta
)
cos
=
np
.
cos
(
theta
)
newContour
=
np
.
zeros_like
(
contour
,
dtype
=
np
.
float
)
for
i
in
range
(
contour
.
shape
[
0
]):
x
:
float
=
cos
*
(
contour
[
i
,
0
,
0
]
-
refPoint
[
0
])
-
sin
*
(
contour
[
i
,
0
,
1
]
-
refPoint
[
1
])
+
refPoint
[
0
]
y
:
float
=
sin
*
(
contour
[
i
,
0
,
0
]
-
refPoint
[
0
])
+
cos
*
(
contour
[
i
,
0
,
1
]
-
refPoint
[
1
])
+
refPoint
[
1
]
newContour
[
i
,
0
,
0
]
=
x
newContour
[
i
,
0
,
1
]
=
y
return
newContour
cythonModules/setup_cython.py
0 → 100644
View file @
6d4cec73
# try:
from
setuptools
import
setup
from
setuptools
import
Extension
from
Cython.Build
import
cythonize
import
numpy
as
np
import
sys
if
len
(
sys
.
argv
)
==
1
:
sys
.
argv
.
append
(
"build_ext"
)
sys
.
argv
.
append
(
"--inplace"
)
ext
=
Extension
(
"rotateContour"
,
[
"rotateContour.pyx"
],
extra_compile_args
=
[
'-O3'
],)
setup
(
name
=
"rotate contour around reference point"
,
ext_modules
=
cythonize
([
ext
],
annotate
=
True
),
# accepts a glob pattern
include_dirs
=
[
np
.
get_include
()]
)
\ No newline at end of file
evaluation.py
View file @
6d4cec73
...
...
@@ -161,7 +161,6 @@ class SampleResult(object):
"""
if
not
self
.
has_attribute
(
newAttribute
):
self
.
attributes
.
append
(
newAttribute
)
print
(
f
'sample
{
self
.
filepath
}
has now attribute
{
newAttribute
}
'
)
def
has_any_attribute
(
self
,
listOfAttributes
:
list
)
->
bool
:
hasAttr
:
bool
=
False
...
...
gui/filterView.py
View file @
6d4cec73
from
PyQt5
import
QtGui
,
QtWidgets
,
QtCore
import
numpy
as
np
import
sys
sys
.
path
.
append
(
"C://Users//xbrjos//Desktop//Python"
)
import
gepard
from
gepard
import
dataset
import
helpers
import
numpy
as
np
from
cythonModules
import
rotateContour
as
rc
class
FilterView
(
QtWidgets
.
QGraphicsView
):
...
...
@@ -14,6 +15,7 @@ class FilterView(QtWidgets.QGraphicsView):
self
.
setWindowTitle
(
'FilterView'
)
self
.
dataset
:
dataset
.
DataSet
=
None
self
.
rotation
:
int
=
0
scene
=
QtWidgets
.
QGraphicsScene
(
self
)
scene
.
setItemIndexMethod
(
QtWidgets
.
QGraphicsScene
.
NoIndex
)
...
...
@@ -47,6 +49,21 @@ class FilterView(QtWidgets.QGraphicsView):
self
.
_update_particle_contours
()
self
.
_fit_to_window
()
@
helpers
.
timingDecorator
def
update_rotation
(
self
,
newRotation
:
int
)
->
None
:
if
newRotation
!=
self
.
rotation
:
angle
:
float
=
np
.
float
(
newRotation
-
self
.
rotation
)
center
:
np
.
ndarray
=
np
.
array
([
self
.
filter
.
circleOffset
[
0
]
+
self
.
filter
.
diameter
/
2
,
self
.
filter
.
circleOffset
[
1
]
+
self
.
filter
.
diameter
/
2
],
dtype
=
np
.
float
)
for
particle
in
self
.
dataset
.
particleContainer
.
particles
:
contour
:
np
.
ndarray
=
particle
.
contour
.
astype
(
np
.
float
)
particle
.
contour
=
rc
.
rotate_contour_around_point
(
contour
,
center
,
angle
)
self
.
_update_particle_contours
()
self
.
rotation
=
newRotation
@
helpers
.
timingDecorator
def
_update_particle_contours
(
self
)
->
None
:
self
.
_remove_particle_contours
()
if
self
.
dataset
is
not
None
:
...
...
gui/mainView.py
View file @
6d4cec73
...
...
@@ -25,14 +25,24 @@ class MainView(QtWidgets.QWidget):
loadDsetBtn
=
QtWidgets
.
QPushButton
(
'Load Dataset'
)
loadDsetBtn
.
released
.
connect
(
self
.
_load_dataset
)
self
.
rotationSpinBox
=
QtWidgets
.
QSpinBox
()
self
.
rotationSpinBox
.
setMinimum
(
0
)
self
.
rotationSpinBox
.
setMaximum
(
359
)
self
.
rotationSpinBox
.
setValue
(
0
)
self
.
rotationSpinBox
.
setMaximumWidth
(
50
)
self
.
rotationSpinBox
.
valueChanged
.
connect
(
self
.
_update_fiter_rotation
)
self
.
controlGroup
=
QtWidgets
.
QGroupBox
()
self
.
controlGroupLayout
=
QtWidgets
.
QHBoxLayout
()
self
.
controlGroup
.
setLayout
(
self
.
controlGroupLayout
)
self
.
controlGroupLayout
.
addWidget
(
loadDsetBtn
)
self
.
controlGroupLayout
.
addWidget
(
QtWidgets
.
QLabel
(
'Filter Rotation'
))
self
.
controlGroupLayout
.
addWidget
(
self
.
rotationSpinBox
)
self
.
controlGroupLayout
.
addWidget
(
QtWidgets
.
QLabel
(
'Select Subsampling Mode:'
))
self
.
controlGroupLayout
.
addWidget
(
self
.
modeSelector
)
self
.
controlGroupLayout
.
addWidget
(
self
.
activeModeControl
)
self
.
controlGroupLayout
.
addStretch
()
self
.
layout
.
addWidget
(
self
.
controlGroup
)
self
.
filterView
=
FilterView
()
...
...
@@ -62,10 +72,11 @@ class MainView(QtWidgets.QWidget):
self
.
activeMode
=
requestedMode
self
.
activeModeControl
=
self
.
activeMode
.
get_control_groupBox
()
self
.
controlGroupLayout
.
insertWidget
(
2
,
self
.
activeModeControl
)
self
.
controlGroupLayout
.
insertWidget
(
3
,
self
.
activeModeControl
)
self
.
activeMode
.
update_measure_viewItems
()
@
helpers
.
timingDecorator
def
_load_dataset
(
self
)
->
None
:
fname
=
QtWidgets
.
QFileDialog
.
getOpenFileName
(
self
,
'Select .pkl file'
,
filter
=
'pkl file (*.pkl)'
)
if
fname
[
0
]
!=
''
:
...
...
@@ -91,6 +102,10 @@ class MainView(QtWidgets.QWidget):
self
.
filterView
.
update_from_dataset
(
dset
)
self
.
activeMode
.
update_measure_viewItems
()
def
_update_fiter_rotation
(
self
):
self
.
filterView
.
update_rotation
(
self
.
rotationSpinBox
.
value
())
self
.
activeMode
.
send_measuredParticles_to_filterview
()
if
__name__
==
'__main__'
:
import
sys
...
...
gui/measureModes.py
View file @
6d4cec73
...
...
@@ -9,6 +9,7 @@ class MeasureMode(QtCore.QObject):
self
.
filterView
:
FilterView
=
relatedFilterView
self
.
uiControls
:
QtWidgets
.
QGroupBox
=
QtWidgets
.
QGroupBox
()
self
.
boxGenerator
:
BoxSelectionSubsamplingMethod
=
None
self
.
subParticles
:
list
=
[]
def
get_control_groupBox
(
self
)
->
QtWidgets
.
QGroupBox
:
return
self
.
uiControls
...
...
@@ -16,7 +17,7 @@ class MeasureMode(QtCore.QObject):
def
update_measure_viewItems
(
self
)
->
None
:
raise
NotImplementedError
def
_
send_measuredParticles_to_filterview
(
self
)
->
None
:
def
send_measuredParticles_to_filterview
(
self
)
->
None
:
if
self
.
boxGenerator
.
particleContainer
is
not
None
:
subParticles
=
self
.
boxGenerator
.
apply_subsampling_method
()
self
.
filterView
.
update_measured_particles
(
subParticles
)
...
...
@@ -44,7 +45,7 @@ class CrossBoxMode(MeasureMode):
topLefts
:
list
=
self
.
boxGenerator
.
get_topLeft_of_boxes
()
boxSize
=
self
.
boxGenerator
.
boxSize
self
.
filterView
.
update_measure_boxes
(
topLefts
,
boxSize
)
self
.
_
send_measuredParticles_to_filterview
()
self
.
send_measuredParticles_to_filterview
()
class
CrossBoxesControls
(
QtWidgets
.
QGroupBox
):
...
...
@@ -103,7 +104,7 @@ class SpiralBoxMode(MeasureMode):
topLefts
:
list
=
self
.
boxGenerator
.
get_topLeft_of_boxes
()
boxSize
=
self
.
boxGenerator
.
boxSize
self
.
filterView
.
update_measure_boxes
(
topLefts
,
boxSize
)
self
.
_
send_measuredParticles_to_filterview
()
self
.
send_measuredParticles_to_filterview
()
class
SpiralBoxControls
(
QtWidgets
.
QGroupBox
):
...
...
helpers.py
View file @
6d4cec73
...
...
@@ -3,24 +3,42 @@ import numpy as np
import
sys
sys
.
path
.
append
(
"C://Users//xbrjos//Desktop//Python"
)
from
gepard
import
dataset
import
time
def
timingDecorator
(
callingFunction
):
"""
A wrapper function for timing the duration of the given function.
:param callingFunction:
:return: wrapped function
"""
def
wrapper
(
*
args
,
**
kwargs
):
t0
=
time
.
time
()
ret
=
callingFunction
(
*
args
,
**
kwargs
)
print
(
f
'
{
callingFunction
.
__name__
}
took
{
np
.
round
(
time
.
time
()
-
t0
,
2
)
}
seconds'
)
return
ret
return
wrapper
class
ParticleBinSorter
(
object
):
def
__init__
(
self
):
super
(
ParticleBinSorter
,
self
).
__init__
()
self
.
bins
=
[
5
,
10
,
20
,
50
,
100
,
200
,
500
]
def
sort_particles_into_bins
(
self
,
particleList
):
particlesInBins
=
self
.
_get_empty_bins
()
for
particle
in
particleList
:
binIndex
=
self
.
_get_binIndex_of_particle
(
particle
)
particlesInBins
[
binIndex
].
append
(
particle
)
return
particlesInBins
def
_get_empty_bins
(
self
):
return
[[]
for
_
in
range
(
len
(
self
.
bins
)
+
1
)]
def
_get_binIndex_of_particle
(
self
,
particle
):
size
=
particle
.
getParticleSize
()
binIndex
=
0
...
...
@@ -114,7 +132,7 @@ def get_polygon_area(polygon: QtGui.QPolygonF) -> float:
return
area
def
get_filterDimensions_from_dataset
(
dataset
)
->
tuple
:
def
get_filterDimensions_from_dataset
(
dataset
:
dataset
.
DataSet
)
->
tuple
:
"""
Processes the datasets boundary items to calculate diameter and offset (coord system offset of circular filter
with respect to actual dataset). This is used to set circular filter dimensions to use in the geometric
...
...
tests/test_cython.py
0 → 100644
View file @
6d4cec73
import
unittest
import
numpy
as
np
from
cythonModules
import
rotateContour
as
rc
class
CythonTester
(
unittest
.
TestCase
):
def
test_rotate_contour
(
self
):
contour
:
np
.
ndarray
=
np
.
array
([[[
0
,
5
]],
[[
5
,
5
]],
[[
5
,
0
]]],
dtype
=
np
.
float
)
refPoint
:
np
.
ndarray
=
np
.
array
([
0
,
0
],
dtype
=
np
.
float
)
angle
:
float
=
90.0
newContour
:
np
.
ndarray
=
rc
.
rotate_contour_around_point
(
contour
,
refPoint
,
angle
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
0
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
1
],
0
)
self
.
assertAlmostEqual
(
newContour
[
1
,
0
,
0
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
1
,
0
,
1
],
5
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
0
],
0
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
1
],
5
)
angle
=
180.0
newContour
=
rc
.
rotate_contour_around_point
(
contour
,
refPoint
,
angle
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
0
],
0
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
1
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
1
,
0
,
0
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
1
,
0
,
1
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
0
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
1
],
0
)
angle
=
270.0
newContour
=
rc
.
rotate_contour_around_point
(
contour
,
refPoint
,
angle
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
0
],
5
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
1
],
0
)
self
.
assertAlmostEqual
(
newContour
[
1
,
0
,
0
],
5
)
self
.
assertAlmostEqual
(
newContour
[
1
,
0
,
1
],
-
5
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
0
],
0
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
1
],
-
5
)
refPoint
=
np
.
array
([
5
,
5
],
dtype
=
np
.
float
)
angle
:
float
=
90.0
newContour
=
rc
.
rotate_contour_around_point
(
contour
,
refPoint
,
angle
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
0
],
5
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
1
],
0
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
0
],
10
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
1
],
5
)
angle
=
180.0
newContour
=
rc
.
rotate_contour_around_point
(
contour
,
refPoint
,
angle
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
0
],
10
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
1
],
5
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
0
],
5
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
1
],
10
)
angle
=
270.0
newContour
=
rc
.
rotate_contour_around_point
(
contour
,
refPoint
,
angle
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
0
],
5
)
self
.
assertAlmostEqual
(
newContour
[
0
,
0
,
1
],
10
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
0
],
0
)
self
.
assertAlmostEqual
(
newContour
[
2
,
0
,
1
],
5
)
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