Commit 15c7be2e authored by Lars Bittrich's avatar Lars Bittrich

further restructuring of code in respect to analysisview; pixelscale modes are...

further restructuring of code in respect to analysisview; pixelscale modes are now handled in dataset; dataset object are now able to be compared for consistency checks later;
parent 58e2489c
...@@ -399,7 +399,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow): ...@@ -399,7 +399,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
self.resultCheckBoxesLayout.addWidget(self.showTotalSelector) self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
#generate new checkboxes #generate new checkboxes
self.polymerCheckBoxes = [] self.polymerCheckBoxes = []
for index, polymer in enumerate(self.datastats.uniquePolymers): uniquePolymers = self.datastats.getUniquePolymers()
for index, polymer in enumerate(uniquePolymers):
self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self)) self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self))
self.polymerCheckBoxes[index].setText(polymer) self.polymerCheckBoxes[index].setText(polymer)
self.resultCheckBoxesLayout.addWidget(self.polymerCheckBoxes[index]) self.resultCheckBoxesLayout.addWidget(self.polymerCheckBoxes[index])
...@@ -427,7 +428,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): ...@@ -427,7 +428,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
self.navigationGroup.setEnabled(True) self.navigationGroup.setEnabled(True)
self.polymerComboBox.currentIndexChanged.disconnect() self.polymerComboBox.currentIndexChanged.disconnect()
self.polymerComboBox.clear() self.polymerComboBox.clear()
self.polymerComboBox.addItems(self.datastats.uniquePolymers) self.polymerComboBox.addItems(uniquePolymers)
self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType) self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
self.polymerIndex = self.polymerComboBox.currentIndex() self.polymerIndex = self.polymerComboBox.currentIndex()
...@@ -489,6 +490,48 @@ class ParticleAnalysis(QtWidgets.QMainWindow): ...@@ -489,6 +490,48 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
self.parent.centerOnRamanIndex(specIndex, centerOn=centerOn, highlightContour=highlightContour) self.parent.centerOnRamanIndex(specIndex, centerOn=centerOn, highlightContour=highlightContour)
self.parent.highLightRamanIndex(specIndex) self.parent.highLightRamanIndex(specIndex)
self.lastSpectrumInFocus = specIndex self.lastSpectrumInFocus = specIndex
def selectContour(self, index, centerOn=True):
uniquePolymers = self.datastats.getUniquePolymers()
if uniquePolymers is not None:
#the index is the contour index, find particle index:
specIndex = self.datastats.particles2spectra[index][0] #select first spectrum of partoicle
self.datastats.currentParticleIndex = index
self.datastats.currentSpectrumIndex = specIndex
selectedPolymer = self.datastats.currentPolymers[specIndex]
try:
self.polymerIndex = uniquePolymers.index(selectedPolymer)
except:
print(selectedPolymer)
raise
#subparticleIndex
partIndicesOfThatPolymer = self.datastats.indices[self.polymerIndex]
subPartInd = partIndicesOfThatPolymer.index(index)
#disconnect analysis widgets:
self.particleSelector.valueChanged.disconnect()
self.spectrumSelector.valueChanged.disconnect()
self.polymerComboBox.currentIndexChanged.disconnect()
#set widgets...
self.particleSelector.setValue(subPartInd+1)
self.particleSelector.setMaximum(len(partIndicesOfThatPolymer))
self.spectrumSelector.setValue(1)
self.spectrumSelector.setMaximum(len(self.datastats.particles2spectra[index]))
selectedPolymer = self.datastats.currentPolymers[specIndex]
self.polymerIndex = uniquePolymers.index(selectedPolymer)
self.polymerComboBox.setCurrentIndex(self.polymerIndex)
#reconnect all widgets:
self.particleSelector.valueChanged.connect(self.selectParticle)
self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
self.updateSpecPlot(centerOn=centerOn)
def displayNewPolymerType(self, resetCurrentIndex=True): def displayNewPolymerType(self, resetCurrentIndex=True):
self.polymerIndex = self.polymerComboBox.currentIndex() self.polymerIndex = self.polymerComboBox.currentIndex()
...@@ -676,6 +719,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow): ...@@ -676,6 +719,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
return color return color
def createPolymerOverlay(self): def createPolymerOverlay(self):
uniquePolymers = self.datastats.getUniquePolymers()
if not self.noOverlayAct.isChecked() and self.datastats.indices is not None: if not self.noOverlayAct.isChecked() and self.datastats.indices is not None:
if len(self.datastats.indices) > 0: if len(self.datastats.indices) > 0:
...@@ -686,9 +730,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow): ...@@ -686,9 +730,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
for index, indexList in enumerate(self.datastats.indices): for index, indexList in enumerate(self.datastats.indices):
if self.fullOverlayAct.isChecked() or (self.selOverlayAct.isChecked() and self.polymerCheckBoxes[index].isChecked()): if self.fullOverlayAct.isChecked() or (self.selOverlayAct.isChecked() and self.polymerCheckBoxes[index].isChecked()):
color = self.getColorFromName(self.datastats.uniquePolymers[index], base255=True) color = self.getColorFromName(uniquePolymers[index], base255=True)
color = QtGui.QColor(color[0], color[1], color[2], alpha=alpha) color = QtGui.QColor(color[0], color[1], color[2], alpha=alpha)
legendItems.append((self.datastats.uniquePolymers[index], color)) legendItems.append((uniquePolymers[index], color))
for i in indexList: for i in indexList:
colorList[i] = color colorList[i] = color
......
...@@ -21,6 +21,19 @@ If not, see <https://www.gnu.org/licenses/>. ...@@ -21,6 +21,19 @@ If not, see <https://www.gnu.org/licenses/>.
import os import os
import numpy as np import numpy as np
import operator import operator
from dataset import loadData
def readDataStats(fname):
ds = loadData(fname)
datastats = DataStats(ds)
datastats.update()
datastats.loadParticleData()
minHQI = datastats.dataset.resultParams['minHQI']
compHQI = datastats.dataset.resultParams['compHQI']
datastats.formatResults(minHQI, compHQI)
datastats.createHistogramData()
return datastats
class DataStats(object): class DataStats(object):
def __init__(self, dataset): def __init__(self, dataset):
...@@ -34,7 +47,6 @@ class DataStats(object): ...@@ -34,7 +47,6 @@ class DataStats(object):
self.currentPolymers = None #list of polymers after setting entries with low hqi to unknown self.currentPolymers = None #list of polymers after setting entries with low hqi to unknown
self.currentAdditives = None #same thing for the additives self.currentAdditives = None #same thing for the additives
self.uniquePolymers = None #list of present polymer types
self.spectra = None #acquired spectra self.spectra = None #acquired spectra
self.indices = None #assignment of what spectra-indices belong to what substance self.indices = None #assignment of what spectra-indices belong to what substance
...@@ -103,7 +115,7 @@ class DataStats(object): ...@@ -103,7 +115,7 @@ class DataStats(object):
def loadParticleData(self): def loadParticleData(self):
self.particlestats = np.array(self.dataset.particlestats) self.particlestats = np.array(self.dataset.particlestats)
pixelscale = (self.dataset.pixelscale_df if self.dataset.imagescanMode == 'df' else self.dataset.pixelscale_bf) pixelscale = self.dataset.getPixelScale()
#convert to mikrometer scale #convert to mikrometer scale
for index in range(len(self.particlestats)): for index in range(len(self.particlestats)):
for subindex in range(5): for subindex in range(5):
...@@ -145,6 +157,11 @@ class DataStats(object): ...@@ -145,6 +157,11 @@ class DataStats(object):
if self.currentAdditives is not None: if self.currentAdditives is not None:
self.currentAdditives[self.addhqis < compHqi] = 'unknown' self.currentAdditives[self.addhqis < compHqi] = 'unknown'
def getUniquePolymers(self):
if self.currentPolymers is None:
return None
return self.uniquePolymers
def createHistogramData(self): def createHistogramData(self):
self.uniquePolymers = np.unique(self.currentPolymers) self.uniquePolymers = np.unique(self.currentPolymers)
self.particleResults = [None]*len(self.particlestats) self.particleResults = [None]*len(self.particlestats)
...@@ -192,4 +209,11 @@ class DataStats(object): ...@@ -192,4 +209,11 @@ class DataStats(object):
self.dataset.resultParams = {'minHQI': minHQI, self.dataset.resultParams = {'minHQI': minHQI,
'compHQI': compHQI} 'compHQI': compHQI}
self.dataset.save() self.dataset.save()
print('saved dataset') print('saved dataset; Valid:', self.testRead())
\ No newline at end of file
def testRead(self):
statsread = readDataStats(self.dataset.fname)
return statsread.__dict__ == self.__dict__
\ No newline at end of file
...@@ -53,6 +53,52 @@ def saveData(dataset, fname): ...@@ -53,6 +53,52 @@ def saveData(dataset, fname):
pickle.dump(dataset, fp, protocol=-1) pickle.dump(dataset, fp, protocol=-1)
dataset.zvalimg = zvalimg dataset.zvalimg = zvalimg
def arrayCompare(a1, a2):
print("array compare")
ind = np.isnan(a1)
if not np.any(ind):
return np.all(a1==a2)
if a1.shape!=a2.shape:
return False
return np.all(a1[~ind]==a2[~ind])
def listCompare(l1, l2):
print("list compare")
if len(l1)!=len(l2):
return False
for l1i, l2i in zip(l1, l2):
if isinstance(l1i, np.ndarray):
if not isinstance(l2i, np.ndarray) or not arrayCompare(l1i, l2i):
return False
elif isinstance(l1i, (list, tuple)):
if not isinstance(l2i, (list, tuple)) or not listCompare(l1i, l2i):
return False
elif l1i!=l2i and ((~np.isnan(l1i)) or (~np.isnan(l2i))):
return False
return True
def recursiveDictCompare(d1, d2):
for key in d1:
if not key in d2:
return False
a = d1[key]
b = d2[key]
print(key, type(a), type(b))
if isinstance(a, np.ndarray):
if not isinstance(b, np.ndarray) or not arrayCompare(a, b):
return False
elif isinstance(a, dict):
if not isinstance(b, dict):
return False
if not recursiveDictCompare(a, b):
return False
elif isinstance(a, (list, tuple)):
if not isinstance(b, (list, tuple)) or not listCompare(a, b):
return False
elif a != b:
return False
return True
class DataSet(object): class DataSet(object):
def __init__(self, fname, newProject=False): def __init__(self, fname, newProject=False):
self.fname = fname self.fname = fname
...@@ -115,6 +161,14 @@ class DataSet(object): ...@@ -115,6 +161,14 @@ class DataSet(object):
self.fname = self.newProject(fname) self.fname = self.newProject(fname)
self.updatePath() self.updatePath()
def __eq__(self, other):
return recursiveDictCompare(self.__dict__, other.__dict__)
def getPixelScale(self, mode=None):
if mode is None:
mode = self.imagescanMode
return (self.pixelscale_df if mode == 'df' else self.pixelscale_bf)
def saveZvalImg(self): def saveZvalImg(self):
if self.zvalimg is not None: if self.zvalimg is not None:
cv2imwrite_fix(self.getZvalImageName(), self.zvalimg) cv2imwrite_fix(self.getZvalImageName(), self.zvalimg)
...@@ -243,8 +297,7 @@ class DataSet(object): ...@@ -243,8 +297,7 @@ class DataSet(object):
p0[1] += self.imagedim_bf[1]/2 p0[1] += self.imagedim_bf[1]/2
return (pixelpos[0]*self.pixelscale_bf + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale_bf) return (pixelpos[0]*self.pixelscale_bf + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale_bf)
else: else:
print('mapToRamanMode not understood') raise ValueError(f'mapToLength mode: {mode} not understood')
return
def mapToLengthRaman(self, pixelpos, microscopeMode='df', noz=False): def mapToLengthRaman(self, pixelpos, microscopeMode='df', noz=False):
p0x, p0y = self.mapToLength(pixelpos, mode = microscopeMode) p0x, p0y = self.mapToLength(pixelpos, mode = microscopeMode)
...@@ -315,9 +368,7 @@ class DataSet(object): ...@@ -315,9 +368,7 @@ class DataSet(object):
saveData(self, self.fname) saveData(self, self.fname)
def saveBackup(self): def saveBackup(self):
# backupNameNotFound = True
inc = 0 inc = 0
# while backupNameNotFound:
while True: while True:
directory = os.path.dirname(self.fname) directory = os.path.dirname(self.fname)
filename = self.name + '_backup_' + str(inc) + '.pkl' filename = self.name + '_backup_' + str(inc) + '.pkl'
...@@ -327,5 +378,4 @@ class DataSet(object): ...@@ -327,5 +378,4 @@ class DataSet(object):
else: else:
saveData(self, path) saveData(self, path)
return filename return filename
# backupNameNotFound = False
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...@@ -22,7 +22,7 @@ import numpy as np ...@@ -22,7 +22,7 @@ import numpy as np
from PyQt5 import QtCore, QtWidgets, QtGui from PyQt5 import QtCore, QtWidgets, QtGui
class SegmentationContours(QtWidgets.QGraphicsItem): class SegmentationContours(QtWidgets.QGraphicsItem):
def __init__(self, parent=None, contours=[], pos=(0,0)): def __init__(self, parent, contours=[], pos=(0,0)):
super().__init__() super().__init__()
self.parent = parent self.parent = parent
self.setPos(pos[0], pos[1]) self.setPos(pos[0], pos[1])
...@@ -122,14 +122,14 @@ class SegmentationContours(QtWidgets.QGraphicsItem): ...@@ -122,14 +122,14 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
for index in self.selectedContours: for index in self.selectedContours:
# partIndex = int(np.where(self.parent.dataset.ramanscansortindex == index)[0]) # partIndex = int(np.where(self.parent.dataset.ramanscansortindex == index)[0])
partIndex = index partIndex = index
assignments.append(self.parent.analysiswidget.particleResults[partIndex]) assignments.append(self.analysiswidget.datastats.particleResults[partIndex])
assignments.append("other") assignments.append("other")
for assignment in np.unique(np.array(assignments)): for assignment in np.unique(np.array(assignments)):
combineActs.append(combineMenu.addAction(assignment)) combineActs.append(combineMenu.addAction(assignment))
reassignActs = [] reassignActs = []
reassignMenu = QtWidgets.QMenu("Reassign particle(s) into") reassignMenu = QtWidgets.QMenu("Reassign particle(s) into")
for polymer in self.parent.analysiswidget.uniquePolymers: for polymer in self.analysiswidget.datastats.getUniquePolymers():
reassignActs.append(reassignMenu.addAction(polymer)) reassignActs.append(reassignMenu.addAction(polymer))
reassignActs.append(reassignMenu.addAction("other")) reassignActs.append(reassignMenu.addAction("other"))
...@@ -156,7 +156,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem): ...@@ -156,7 +156,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
# QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...") # QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
# return # return
self.parent.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment) self.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)
elif action in reassignActs: elif action in reassignActs:
newAssignment = action.text() newAssignment = action.text()
...@@ -164,7 +164,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem): ...@@ -164,7 +164,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
# QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...") # QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
# return # return
self.parent.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment) self.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)
class FitPosIndicator(QtWidgets.QGraphicsItem): class FitPosIndicator(QtWidgets.QGraphicsItem):
......
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