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Commit fa14c5fa authored by Josef Brandt's avatar Josef Brandt
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applying subsampling now is also used for updating the gui 

Also, it now only returns the list of measured particles..
parent 95a7feb0
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Showing with 145 additions and 76 deletions
evaluation.py
View file @ fa14c5fa
......@@ -5,11 +5,30 @@ Created on Wed Jan 22 13:57:28 2020
@author: luna
"""
import pickle
import os
from helpers import ParticleBinSorter
class ResultComparer(object):
class ResultObject(object):
"""
An object the actually stores all generated results per sample and can update and report on them.
"""
def __init__(self, filepath: str):
super(ResultObject, self).__init__()
self.filepath: str = filepath
print(self.sampleName)
# noinspection PyTypeChecker
@property
def sampleName(self) -> str:
return os.path.basename(self.filepath).split('.')[0]
class ResultComparer(object):
def _get_mp_count_error_per_bin(self, allParticles, subParticles, fractionMeasured):
binSorter = ParticleBinSorter()
allParticlesInBins = binSorter.sort_particles_into_bins(allParticles)
......@@ -47,4 +66,4 @@ class ResultComparer(object):
numMPParticles += 1
break
return numMPParticles
\ No newline at end of file
return numMPParticles
geometricMethods.py
View file @ fa14c5fa
......@@ -22,20 +22,38 @@ class BoxSelectionSubsamplingMethod(SubsamplingMethod):
def filterArea(self) -> float:
return np.pi * (self.filterDiameter / 2) ** 2
def apply_subsampling_method(self) -> tuple:
def apply_subsampling_method(self) -> list:
def distanceToCnt(topleft: tuple):
return abs(topleft[0] - cntStart[0]) + abs(topleft[1] - cntStart[1])
subParticles: list = []
topLefts: list = self.get_topLeft_of_boxes()
boxSize = self.boxSize
boxWidthHeight: tuple = (self.boxSize, self.boxSize)
for particle in self.particleContainer.particles:
for topLeft in topLefts:
if box_overlaps_contour(topLeft, (boxSize, boxSize), particle.contour, self.offset):
cntStart: tuple = (particle.contour[0, 0, 0], particle.contour[0, 0, 1])
sortedTopLefts = sorted(topLefts, key=distanceToCnt)
for topLeftXY in sortedTopLefts:
if helpers.box_overlaps_contour(topLeftXY, boxWidthHeight, particle.contour):
subParticles.append(particle)
break
return self.fraction, subParticles
return subParticles
def get_topLeft_of_boxes(self) -> list:
raise NotImplementedError
def _apply_offset_to_toplefts(self, topLefts: list) -> list:
"""
Applies the filter offset to the calculated topLefts of the measure boxes.
:param topLefts:
:return:
"""
newTopLefts: list = []
for topLeft in topLefts:
newTopLefts.append((topLeft[0] + self.offset[0], topLeft[1] + self.offset[1]))
return newTopLefts
class BoxSelectionCreator(object):
def __init__(self, dataset: dataset.DataSet):
......@@ -122,7 +140,7 @@ class CrossBoxSelector(BoxSelectionSubsamplingMethod):
if i != self.numBoxesAcross // 2:
topLeftCorners.append((xStartCoordinates[i], middleYCoordinate))
return topLeftCorners
return self._apply_offset_to_toplefts(topLeftCorners)
def get_maximum_achievable_fraction(self) -> float:
"""
......@@ -216,7 +234,7 @@ class SpiralSelector(BoxSelectionSubsamplingMethod):
boxDistance *= 1.05
topLefts = self._move_and_scale_toplefts(topLefts)
return topLefts
return self._apply_offset_to_toplefts(topLefts)
def _move_and_scale_toplefts(self, topLefts: list) -> list:
"""
......
gui/filterView.py
View file @ fa14c5fa
......@@ -32,36 +32,20 @@ class FilterView(QtWidgets.QGraphicsView):
def update_measure_boxes(self, topLefts: list, boxSize: float) -> None:
self._remove_measure_boxes()
offset = self.filter.circleOffset
for x, y in topLefts:
newBox: MeasureBoxGraphItem = MeasureBoxGraphItem(x+offset[0], y+offset[1], boxSize, boxSize)
newBox: MeasureBoxGraphItem = MeasureBoxGraphItem(x, y, boxSize, boxSize)
self.measuringBoxes.append(newBox)
self.scene().addItem(newBox)
self._update_measured_contours()
def _remove_measure_boxes(self) -> None:
for item in self.measuringBoxes:
self.scene().removeItem(item)
self.measuringBoxes = []
def load_and_update_from_dataset(self, fname: str) -> None:
try:
self.dataset = dataset.loadData(fname)
except IndexError:
self.dataset = None
QtWidgets.QMessageBox.critical(self, 'Index Error', 'Unable to load dataset..')
if self.dataset is not None:
offset, diameter, widthHeight = helpers.get_filterDimensions_from_dataset(self.dataset)
offsetx = helpers.convert_length_to_pixels(self.dataset, offset[0])
offsety = helpers.convert_length_to_pixels(self.dataset, offset[1])
diameter = helpers.convert_length_to_pixels(self.dataset, diameter)
width = helpers.convert_length_to_pixels(self.dataset, widthHeight[0])
height = helpers.convert_length_to_pixels(self.dataset, widthHeight[1])
self.filter.update_filterSize(width, height, diameter, (offsetx, offsety))
self._update_particle_contours()
self._fit_to_window()
def update_from_dataset(self, dset: dataset.DataSet) -> None:
self.dataset = dset
self._update_particle_contours()
self._fit_to_window()
def _update_particle_contours(self) -> None:
self._remove_particle_contours()
......@@ -76,22 +60,10 @@ class FilterView(QtWidgets.QGraphicsView):
self.scene().removeItem(cntItem)
self.contourItems = []
def _update_measured_contours(self) -> None:
def distanceToCnt(box: MeasureBoxGraphItem):
return abs(box.posX - cntStart[0]) + abs(box.posY - cntStart[1])
for contourItem in self.contourItems:
contourItem.isMeasured = False
cntStart: tuple = (contourItem.contourData[0, 0, 0], contourItem.contourData[0, 0, 1])
sortedmeasBoxes = sorted(self.measuringBoxes, key=distanceToCnt)
for measBox in sortedmeasBoxes:
topLeftXY = (measBox.posX, measBox.posY)
boxWidthHeight = (measBox.width, measBox.height)
if helpers.box_overlaps_contour(topLeftXY, boxWidthHeight, contourItem.contourData):
contourItem.isMeasured = True
contourItem.update()
break
def update_measured_particles(self, measuredParticles: list) -> None:
measuredIndices: list = [particle.index for particle in measuredParticles]
for index, contourItem in enumerate(self.contourItems):
contourItem.isMeasured = (index in measuredIndices)
def wheelEvent(self, event: QtGui.QWheelEvent) -> None:
factor: float = 1.01 ** (event.angleDelta().y() / 8)
......
gui/mainView.py
View file @ fa14c5fa
from PyQt5 import QtWidgets
import sys
sys.path.append("C://Users//xbrjos//Desktop//Python")
import gepard
from gepard import dataset
from gui.filterView import FilterView
from gui.measureModes import MeasureMode, CrossBoxMode, CrossBoxesControls, SpiralBoxMode
import helpers
class MainView(QtWidgets.QWidget):
......@@ -64,8 +69,27 @@ class MainView(QtWidgets.QWidget):
def _load_dataset(self) -> None:
fname = QtWidgets.QFileDialog.getOpenFileName(self, 'Select .pkl file', filter='pkl file (*.pkl)')
if fname[0] != '':
self.filterView.load_and_update_from_dataset(fname[0])
self.activeMode.update_measure_viewItems()
try:
dset: dataset.DataSet = dataset.loadData(fname[0])
except IndexError:
dset = None
QtWidgets.QMessageBox.critical(self, 'Index Error', 'Unable to load dataset..')
if dset is not None:
offset, diameter, widthHeight = helpers.get_filterDimensions_from_dataset(dset)
offsetx = helpers.convert_length_to_pixels(dset, offset[0])
offsety = helpers.convert_length_to_pixels(dset, offset[1])
diameter = helpers.convert_length_to_pixels(dset, diameter)
width = helpers.convert_length_to_pixels(dset, widthHeight[0])
height = helpers.convert_length_to_pixels(dset, widthHeight[1])
self.filterView.filter.update_filterSize(width, height, diameter, (offsetx, offsety))
for mode in self.measureModes.values():
mode.boxGenerator.particleContainer = dset.particleContainer
mode.boxGenerator.offset = (offsetx, offsety)
self.filterView.update_from_dataset(dset)
self.activeMode.update_measure_viewItems()
if __name__ == '__main__':
......
gui/measureModes.py
View file @ fa14c5fa
from PyQt5 import QtCore, QtWidgets
from gui.filterView import FilterView, MeasureBoxGraphItem
from geometricMethods import CrossBoxSelector, SpiralSelector
from geometricMethods import BoxSelectionSubsamplingMethod, CrossBoxSelector, SpiralSelector
class MeasureMode(QtCore.QObject):
def __init__(self, relatedFilterView: FilterView):
super(MeasureMode, self).__init__()
self.filterView = relatedFilterView
self.filterView: FilterView = relatedFilterView
self.uiControls: QtWidgets.QGroupBox = QtWidgets.QGroupBox()
self.boxGenerator: BoxSelectionSubsamplingMethod = None
def get_control_groupBox(self) -> QtWidgets.QGroupBox:
return self.uiControls
......@@ -15,29 +16,35 @@ class MeasureMode(QtCore.QObject):
def update_measure_viewItems(self) -> None:
raise NotImplementedError
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)
class CrossBoxMode(MeasureMode):
def __init__(self, *args):
super(CrossBoxMode, self).__init__(*args)
self.uiControls = CrossBoxesControls(self)
self.crossBoxGenerator: CrossBoxSelector = CrossBoxSelector(None)
self.boxGenerator: CrossBoxSelector = CrossBoxSelector(None)
self.update_measure_viewItems()
def update_measure_viewItems(self) -> None:
self.crossBoxGenerator.filterDiameter = self.filterView.filter.diameter
self.crossBoxGenerator.numBoxesAcross = int(self.uiControls.numBoxesSelector.currentText())
self.boxGenerator.filterDiameter = self.filterView.filter.diameter
self.boxGenerator.numBoxesAcross = int(self.uiControls.numBoxesSelector.currentText())
desiredCoverage: int = self.uiControls.coverageSpinbox.value()
maxCoverage: int = int(self.crossBoxGenerator.get_maximum_achievable_fraction() * 100)
maxCoverage: int = int(self.boxGenerator.get_maximum_achievable_fraction() * 100)
self.uiControls.set_to_max_possible_coverage(maxCoverage)
if desiredCoverage > maxCoverage:
desiredCoverage = maxCoverage
self.crossBoxGenerator.fraction = desiredCoverage / 100
self.boxGenerator.fraction = desiredCoverage / 100
topLefts: list = self.crossBoxGenerator.get_topLeft_of_boxes()
boxSize = self.crossBoxGenerator.boxSize
topLefts: list = self.boxGenerator.get_topLeft_of_boxes()
boxSize = self.boxGenerator.boxSize
self.filterView.update_measure_boxes(topLefts, boxSize)
self._send_measuredParticles_to_filterview()
class CrossBoxesControls(QtWidgets.QGroupBox):
......@@ -84,18 +91,19 @@ class SpiralBoxMode(MeasureMode):
def __init__(self, *args):
super(SpiralBoxMode, self).__init__(*args)
self.uiControls: SpiralBoxControls = SpiralBoxControls(self)
self.spiralBoxGenerator: SpiralSelector = SpiralSelector(None)
self.boxGenerator: SpiralSelector = SpiralSelector(None)
self.update_measure_viewItems()
def update_measure_viewItems(self) -> None:
self.spiralBoxGenerator.filterDiameter = self.filterView.filter.diameter
self.boxGenerator.filterDiameter = self.filterView.filter.diameter
self.spiralBoxGenerator.numBoxes = self.uiControls.numBoxesSpinbox.value()
self.spiralBoxGenerator.fraction = self.uiControls.coverageSpinbox.value() / 100
self.boxGenerator.numBoxes = self.uiControls.numBoxesSpinbox.value()
self.boxGenerator.fraction = self.uiControls.coverageSpinbox.value() / 100
topLefts: list = self.spiralBoxGenerator.get_topLeft_of_boxes()
boxSize = self.spiralBoxGenerator.boxSize
topLefts: list = self.boxGenerator.get_topLeft_of_boxes()
boxSize = self.boxGenerator.boxSize
self.filterView.update_measure_boxes(topLefts, boxSize)
self._send_measuredParticles_to_filterview()
class SpiralBoxControls(QtWidgets.QGroupBox):
......
methods.py
View file @ fa14c5fa
......@@ -24,12 +24,12 @@ class SubsamplingMethod(object):
"""
raise NotImplementedError
def apply_subsampling_method(self) -> tuple:
def apply_subsampling_method(self) -> list:
"""
Takes all particles from the supplied particle conatiner and returns a new list of particles that
were measured by applying that subsampling procedure. Also, the actualy measured fraction is returned.
(The desired fraction may not always be achievable)
:returns actuallyMeasuredFraction, listOfSubParticles:
:returns listOfActuallyMeasuredParticles:
"""
raise NotImplementedError
......@@ -39,11 +39,11 @@ class RandomSampling(SubsamplingMethod):
def label(self) -> str:
return 'Random Subsampling'
def apply_subsampling_method(self):
def apply_subsampling_method(self) -> list:
numOrigParticles = len(self.particleContainer.particles)
numParticles = self._get_number_of_random_particles(numOrigParticles)
subParticles = random.sample(self.particleContainer.particles, numParticles)
return self.fraction, subParticles
return subParticles
def _get_number_of_random_particles(self, numTotalParticles):
return np.int(np.ceil(numTotalParticles * self.fraction))
......@@ -60,12 +60,12 @@ class IvlevaSubsampling(SubsamplingMethod):
def label(self) -> str:
return 'Random fraction, Anger et al.'
def apply_subsampling_method(self):
def apply_subsampling_method(self) -> list:
N = self.particleContainer.getNumberOfParticles()
numParticlesMeasured = self._get_ivleva_fraction(N)
subParticles = random.sample(self.particleContainer.particles, numParticlesMeasured)
fractionMeasured = numParticlesMeasured/N
return fractionMeasured, subParticles
return subParticles
def _get_ivleva_fraction(self, N):
P = self.estimatedMPFraction
......@@ -83,13 +83,13 @@ class SizeBinFractioning(SubsamplingMethod):
def label(self) -> str:
return 'SizeBin Random Subsampling'
def apply_subsampling_method(self):
def apply_subsampling_method(self) -> list:
subParticlesPerBin: list = self._get_subParticles_per_bin(self.particleContainer.particles)
subParticles: list = []
for subParticleList in subParticlesPerBin:
for particle in subParticleList:
subParticles.append(particle)
return self.fraction, subParticles
return subParticles
def _get_subParticles_per_bin(self, particleList: list):
particlesInBins: list = self.sorter.sort_particles_into_bins(particleList)
......
subsampling.py
View file @ fa14c5fa
......@@ -9,7 +9,7 @@ import gepardevaluation
from methods import IvlevaSubsampling, RandomSampling, SizeBinFractioning
from geometricMethods import BoxSelectionCreator
from helpers import ParticleBinSorter
from evaluation import ResultComparer
from evaluation import ResultComparer, ResultObject
"""
......@@ -28,8 +28,9 @@ workingFiles.append(r'C:\Users\xbrjos\Desktop\temp MP\190201_BSB_Stroomi_ds2_R1_
# fname: str = r'C:\Users\xbrjos\Desktop\temp MP\KWS_CT_3_ds1_all_10_2\KWS_CT_3_ds1_all_10_2.pkl'
for index, fname in enumerate(workingFiles):
dset = dataset.loadData(fname)
print('loaded dataset', fname)
# dset = dataset.loadData(fname)
newObj: ResultObject = ResultObject(fname)
# print('loaded dataset', fname)
# boxCreator = BoxSelectionCreator(dset)
# center, size = boxCreator.get_filterDimensions_from_dataset()
......
tests/test_geometricMethods.py
View file @ fa14c5fa
import sys
import unittest
import numpy as np
from geometricMethods import CrossBoxSelector, SpiralSelector, BoxSelectionCreator
from geometricMethods import BoxSelectionSubsamplingMethod, CrossBoxSelector, SpiralSelector, BoxSelectionCreator
sys.path.append("C://Users//xbrjos//Desktop//Python")
from gepard import dataset
class TestBoxSelector(unittest.TestCase):
def setUp(self) -> None:
self.boxSelector: BoxSelectionSubsamplingMethod = BoxSelectionSubsamplingMethod(None)
def test_apply_offset_to_toplefts(self):
topLefts = [(0, 0), (10, 10), (-5, -5), (0, 20)]
self.boxSelector.offset = (0, 0)
newTopLefts: list = self.boxSelector._apply_offset_to_toplefts(topLefts)
self.assertEqual(newTopLefts[0], (0, 0))
self.assertEqual(newTopLefts[1], (10, 10))
self.assertEqual(newTopLefts[2], (-5, -5))
self.assertEqual(newTopLefts[3], (0, 20))
self.boxSelector.offset = (10, 0)
newTopLefts: list = self.boxSelector._apply_offset_to_toplefts(topLefts)
self.assertEqual(newTopLefts[0], (10, 0))
self.assertEqual(newTopLefts[1], (20, 10))
self.assertEqual(newTopLefts[2], (5, -5))
self.assertEqual(newTopLefts[3], (10, 20))
self.boxSelector.offset = (10, -20)
newTopLefts: list = self.boxSelector._apply_offset_to_toplefts(topLefts)
self.assertEqual(newTopLefts[0], (10, -20))
self.assertEqual(newTopLefts[1], (20, -10))
self.assertEqual(newTopLefts[2], (5, -25))
self.assertEqual(newTopLefts[3], (10, 0))
class TestSelectCrossBoxes(unittest.TestCase):
def setUp(self) -> None:
self.crossBoxSelector = CrossBoxSelector(None)
......
tests/test_methods.py
View file @ fa14c5fa
......@@ -41,7 +41,7 @@ class TestIvleva(unittest.TestCase):
ivlevaSampling = IvlevaSubsampling(self.particleContainer, sigma=1.65, mpFraction=0.05, errorMargin=0.1)
numParticles = ivlevaSampling._get_ivleva_fraction(1000)
ivlevaFraction, ivlevaParticles = ivlevaSampling.apply_subsampling_method()
ivlevaParticles = ivlevaSampling.apply_subsampling_method()
self.assertEqual(len(ivlevaParticles), numParticles)
......
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