def calc_foci_in_dirlist(dir_path, dir_list, nuclei_name=u'3DAPI.TIF', foci_name=u'3FITС.TIF', outfile = u'result.txt',\
sensitivity = 8., min_cell_size = 1500, peak_min_val_perc = 60, foci_min_val_perc = 90,\
foci_radius = 10, foci_min_level_on_bg = 40, foci_rescale_min = None, foci_rescale_max = None,\
nuclei_color = 0.66, foci_color = 0.33):
'''Calculates foci from dir'''
dirs_with_images = dir_list
pre_image_dirs = [image_dir for image_dir in dirs_with_images if \
(os.path.isfile(os.path.join(image_dir,nuclei_name)) and os.path.isfile(os.path.join(image_dir, foci_name)))]
image_dirs = [
pic_an.image_dir(image_dir, nuclei_name, foci_name)
for image_dir in pre_image_dirs
]
path1, name2 = os.path.split(dir_path)
name1 = os.path.split(path1)[1]
print name1, name2, path1
name = name1 + '_' + name2
absoutfile = os.path.join(dir_path, outfile)
print name
cell_set = pic_an.cell_set(name=name, cells=[])
remained = len(image_dirs)
print "We have", remained, 'images to load for', name
print "Image loading have started for", name
for image_dir in image_dirs:
image_dir.load_separate_images(sensitivity, min_cell_size)
remained -= 1
if remained == 0:
print "Image loading have finished for", name
else:
print remained, 'images remained to load for', name
cell_set.extend(image_dir)
if len(cell_set.cells) == 0:
print "There are no cells in the images from ", dir_path
return
print "We have", len(cell_set.cells), "cells to analyze for", name
cell_set.rescale_nuclei()
cell_set.rescale_foci((foci_rescale_min, foci_rescale_max))
cell_set.calculate_foci(peak_min_val_perc, foci_min_val_perc, foci_radius,
foci_min_level_on_bg)
cell_set.calculate_foci_parameters()
cell_set.write_parameters(absoutfile)
for image_dir in image_dirs:
image_dir.write_all_pic_files(nuclei_color, foci_color)
def getScaleFromSelected(self):
self.cell_set = pic_an.cell_set(name=self.workDir, cells=[])
tasksize=len(self.getCheckedPaths())
self.parent.pbar.show()
pbarvalue=0
self.parent.pbar.setValue(pbarvalue)
pbarstep = (100 - 10 )/ tasksize
if len(self.folderWidgets) != 0:
for i in xrange(0,len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState() == QtCore.Qt.Checked :
self.imageDirs[i].detect_cells(self.parent.settings.sensitivity,
self.parent.settings.min_cell_size, load_foci=True)
self.cell_set.extend(self.imageDirs[i])
pbarvalue+=pbarstep
self.parent.pbar.setValue(pbarvalue)
(self.parent.settings.foci_rescale_min,
self.parent.settings.foci_rescale_max) = self.cell_set.get_foci_rescale_values()
print 'Foci rescale values changed to:\nmin: ' + str(self.parent.settings.foci_rescale_min) \
+ '\nmax: '+ str(self.parent.settings.foci_rescale_max)
self.parent.pbar.setValue(100)
def getScaleFromSelected(self):
self.cell_set = pic_an.cell_set(name=self.workDir, cells=[])
tasksize = len(self.getCheckedPaths())
self.parent.pbar.show()
pbarvalue = 0
self.parent.pbar.setValue(pbarvalue)
pbarstep = (100 - 10) / tasksize
if len(self.folderWidgets) != 0:
for i in xrange(0, len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState(
) == QtCore.Qt.Checked:
self.imageDirs[i].detect_cells(
self.parent.settings.sensitivity,
self.parent.settings.min_cell_size,
load_foci=True)
self.cell_set.extend(self.imageDirs[i])
pbarvalue += pbarstep
self.parent.pbar.setValue(pbarvalue)
(self.parent.settings.foci_rescale_min,
self.parent.settings.foci_rescale_max
) = self.cell_set.get_foci_rescale_values()
print 'Foci rescale values changed to:\nmin: ' + str(self.parent.settings.foci_rescale_min) \
+ '\nmax: '+ str(self.parent.settings.foci_rescale_max)
self.parent.pbar.setValue(100)
def runCalc(self):
dir_path = self.fileMenuArea.getWorkDir()
dirs_with_images = self.fileMenuArea.getCheckedPaths()
if len(dirs_with_images) == 0 :
return
else:
if (self.oldDirsWithImages == dirs_with_images) & self.lastCalc & (not(self.settingsChanged)):
print "No changes in selection"
else:
pre_image_dirs = [image_dir for image_dir in dirs_with_images if \
(os.path.isfile(os.path.join(image_dir,self.nuclei_name)) and os.path.isfile(os.path.join(image_dir, self.foci_name)))]
image_dirs = [pic_an.image_dir(image_dir, self.nuclei_name, self.foci_name) for image_dir in pre_image_dirs]
name = unicode(QtCore.QDir(dir_path).dirName())
absoutfile = os.path.join(dir_path,unicode(self.outfile))
print absoutfile
cell_set = pic_an.cell_set(name=name, cells=[])
remained = len(image_dirs)
if remained != 0:
pbarval = 0
self.pbar.show()
self.pbar.setValue(pbarval)
pbarstep = (100 - 10 )/ remained
print "We have", remained, 'images to load for', name
print "Image loading have started for", name
for image_dir in image_dirs:
image_dir.load_separate_images(self.sensitivity, self.min_cell_size)
pbarval +=pbarstep
self.pbar.setValue(pbarval)
remained -= 1
if remained == 0:
print "Image loading have finished for", name
else:
print remained, 'images remained to load for', name
cell_set.extend(image_dir)
if len(cell_set.cells) == 0:
print "There are no cells in the images from ", dir_path
return
print "We have", len(cell_set.cells), "cells to analyze for", name
cell_set.rescale_nuclei()
cell_set.rescale_foci((self.foci_rescale_min, self.foci_rescale_max))
self.oldFoci_rescale_min, self.oldFoci_rescale_max = cell_set.get_foci_rescale_values()
cell_set.calculate_foci(self.peak_min_val_perc, self.foci_min_val_perc, self.foci_radius, self.foci_min_level_on_bg)
cell_set.calculate_foci_parameters()
cell_set.write_parameters(absoutfile)
params = cell_set.get_parameters()
self.statusArea.hide()
self.statusArea.setItem(0,0,QtGui.QTableWidgetItem(str(params[0])))
for i in xrange(1,13):
self.statusArea.setItem((i+1)%2,(i+1)//2,QtGui.QTableWidgetItem(str(params[i])))
#self.update()
for image_dir in image_dirs:
image_dir.write_all_pic_files(self.nuclei_color, self.foci_color)
self.statusArea.show()
self.pbar.setValue(100)
self.updateImages()
self.fileMenuArea.updateWorkDir()
self.fileMenuArea.setCheckedFromPaths(dirs_with_images)
self.oldDirsWithImages = dirs_with_images
self.lastCalc=True
self.settingsChanged=False
else:
print "no images is dataset"
def getScale(self):
dir_path = self.fileMenuArea.getWorkDir()
dirs_with_images = self.fileMenuArea.getCheckedPaths()
if len(dirs_with_images) == 0 :
return
else:
if (self.oldDirsWithImages == dirs_with_images) & (not(self.settingsChanged)):
print "No changes in selection, setting values from previous calc"
self.foci_rescale_min = self.oldFoci_rescale_min
self.foci_rescale_max = self.oldFoci_rescale_max
print "Foci rescale min max", self.foci_rescale_min, self.foci_rescale_max
else:
### move to folderMenu widget?
pre_image_dirs = [image_dir for image_dir in dirs_with_images if \
(os.path.isfile(os.path.join(image_dir,self.nuclei_name)) and os.path.isfile(os.path.join(image_dir, self.foci_name)))]
image_dirs = [pic_an.image_dir(image_dir, self.nuclei_name, self.foci_name) for image_dir in pre_image_dirs]
#########################
name = unicode(QtCore.QDir(dir_path).dirName())
cell_set = pic_an.cell_set(name=name, cells=[])
remained = len(image_dirs)
if remained != 0:
pbarval = 0
self.pbar.show()
self.pbar.setValue(pbarval)
pbarstep = (100 - 10 )/ remained
print "We have", remained, 'images to load for', name
print "Image loading have started for", name
for image_dir in image_dirs:
image_dir.load_separate_images(self.sensitivity, self.min_cell_size)
pbarval +=pbarstep
self.pbar.setValue(pbarval)
remained -= 1
if remained == 0:
print "Image loading have finished for", name
else:
print remained, 'images remained to load for', name
cell_set.extend(image_dir)
if len(cell_set.cells) == 0:
print "There are no cells in the images from ", dir_path
return
print "We have", len(cell_set.cells), "cells to analyze for", name
cell_set.rescale_foci((None, None))
self.foci_rescale_min, self.foci_rescale_max = cell_set.get_foci_rescale_values()
self.oldFoci_rescale_min, self.oldFoci_rescale_max = self.foci_rescale_min, self.foci_rescale_max
print "Foci rescale min max", self.foci_rescale_min, self.foci_rescale_max
self.pbar.setValue(100)
self.oldDirsWithImages = dirs_with_images
self.lastCalc=False
self.settingsChanged=False
else:
print "no images is dataset"
def openWorkDir(self, workdir=None):
if not (workdir):
workdir = QtGui.QFileDialog.getExistingDirectory(
directory=self.workDir)
if workdir != "":
self.parent.workDir = unicode(workdir)
if workdir != "":
self.workDir = unicode(workdir)
for i in reversed(range(self.folderLayout.count())):
self.folderLayout.itemAt(i).widget().setParent(None)
self.selectedImage = ""
self.selectedImageDir = ""
self.checkedPaths = []
self.nameList = []
folderIterator = QtCore.QDirIterator(
self.workDir, QtCore.QDir.Dirs | QtCore.QDir.NoDotAndDotDot)
while folderIterator.hasNext():
imageQDir = QtCore.QDir(folderIterator.next())
imageList = imageQDir.entryList(
["*.TIF", "*.tif", "*.jpg", "*.JPG", "*.BMP", "*.bmp"])
for name in imageList:
if not (name in self.nameList):
self.nameList.append(unicode(name))
[
self.parent.nuclNameComboBox.removeItem(0)
for i in xrange(self.parent.nuclNameComboBox.count())
]
self.parent.nuclNameComboBox.addItems(self.nameList)
if self.parent.settings.nuclei_name in self.nameList:
#print self.parent.nuclNameComboBox.itemText(1)
self.parent.nuclNameComboBox.setCurrentIndex(
self.parent.nuclNameComboBox.findText(
self.parent.settings.nuclei_name))
else:
self.parent.nuclNameComboBox.setCurrentIndex(0)
self.parent.settings.nuclei_name = self.nameList[0]
[
self.parent.fociNameComboBox.removeItem(1)
for i in xrange(1, self.parent.fociNameComboBox.count())
]
self.parent.fociNameComboBox.addItems(self.nameList)
if self.parent.settings.foci_name in self.nameList:
self.parent.fociNameComboBox.setCurrentIndex(
self.parent.fociNameComboBox.findText(
self.parent.settings.foci_name))
else:
self.parent.fociNameComboBox.setCurrentIndex(0)
self.parent.settings.foci_name = '--None--'
self.checkAllBox = QtGui.QCheckBox('Check/Uncheck All', self)
self.checkAllBox.setChecked(True)
self.checkAllBox.stateChanged.connect(lambda: (self.checkAll(
) if self.checkAllBox.isChecked() else self.unCheckAll()))
self.folderLayout.addWidget(self.checkAllBox)
self.folderWidgets = []
self.imageDirs = []
self.cell_set = pic_an.cell_set(name=self.workDir, cells=[])
i = 0
folderIterator = QtCore.QDirIterator(
self.workDir, QtCore.QDir.Dirs | QtCore.QDir.NoDotAndDotDot)
while folderIterator.hasNext():
imageQDir = QtCore.QDir(folderIterator.next())
nucleiPath = imageQDir.absolutePath() + QtCore.QDir.separator(
) + self.parent.settings.nuclei_name
fociPath = imageQDir.absolutePath() + QtCore.QDir.separator(
) + self.parent.settings.foci_name
if ((self.parent.settings.foci_name == '--None--') &
(QtCore.QFile(nucleiPath).exists())):
self.imageDirs.append(
pic_an.image_dir(
unicode(imageQDir.absolutePath()),
unicode(self.parent.settings.nuclei_name)))
self.folderWidgets.append(imageFolderWidget(imageQDir))
self.folderLayout.addWidget(self.folderWidgets[-1])
self.folderWidgets[-1].signal_hideall.connect(
self.hideAllImageLabels)
############
self.folderWidgets[-1].signal_show_image.connect(
lambda key=i: self.updateImage(key))
self.folderWidgets[-1].signal_show_all_images.connect(
lambda key=i: self.updateImages(key))
############
i += 1
elif ((QtCore.QFile(fociPath).exists()) &
(QtCore.QFile(nucleiPath).exists())):
self.imageDirs.append(
pic_an.image_dir(
unicode(imageQDir.absolutePath()),
unicode(self.parent.settings.nuclei_name),
unicode(self.parent.settings.foci_name)))
self.folderWidgets.append(imageFolderWidget(imageQDir))
self.folderLayout.addWidget(self.folderWidgets[-1])
self.folderWidgets[-1].signal_hideall.connect(
self.hideAllImageLabels)
############
self.folderWidgets[-1].signal_show_image.connect(
lambda key=i: self.updateImage(key))
self.folderWidgets[-1].signal_show_all_images.connect(
lambda key=i: self.updateImages(key))
############
i += 1
print str(len(self.imageDirs)) + ' dirs found in working directory'
try:
self.updateImages(0)
except IndexError:
self.signal_update_images.emit()
def calculateSelected(self):
self.parent.outfileButton.setEnabled(False)
self.parent.singleCellOutputBox.setEnabled(False)
name = QtCore.QDir(self.workDir).dirName()
self.cell_set = pic_an.cell_set(name=name, cells=[])
tasksize = len(self.getCheckedPaths())
print("We have %d images to load for %s" % (tasksize, name))
self.parent.pbar.show()
pbarvalue = 0
self.parent.pbar.setValue(pbarvalue)
pbarstep = (100 - 10) / tasksize
# Calculation
if len(self.folderWidgets) != 0:
if self.parent.settings.foci_name == '--None--':
for i in xrange(0, len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState(
) == QtCore.Qt.Checked:
self.imageDirs[i].detect_cells(
self.parent.settings.sensitivity,
self.parent.settings.min_cell_size,
load_foci=False)
self.cell_set.extend(self.imageDirs[i])
tasksize -= 1
if tasksize == 0:
print("Image loading has finished for %s" % name)
else:
print('%d images remained to load for %s' %
(tasksize, name))
pbarvalue += pbarstep
self.parent.pbar.setValue(pbarvalue)
for i in xrange(0, len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState(
) == QtCore.Qt.Checked:
self.imageDirs[i].write_all_pic_files(
self.parent.settings.nuclei_color,
self.parent.settings.foci_color)
self.updateParamsTable()
self.updateAllImageLabels()
self.refreshImages()
self.parent.pbar.setValue(100)
self.parent.outfileButton.setEnabled(True)
self.parent.singleCellOutputBox.setEnabled(True)
else:
for i in xrange(0, len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState(
) == QtCore.Qt.Checked:
self.imageDirs[i].detect_cells(
self.parent.settings.sensitivity,
self.parent.settings.min_cell_size,
load_foci=True)
self.cell_set.extend(self.imageDirs[i])
tasksize -= 1
if tasksize == 0:
print("Image loading has finished for %s" % name)
else:
print('%d images remained to load for %s' %
(tasksize, name))
pbarvalue += pbarstep
self.parent.pbar.setValue(pbarvalue)
if len(self.cell_set.cells) == 0:
print("No cells were detected in %s" % name)
return
print("We have %d cells to analyze for %s" %
(len(self.cell_set.cells), name))
self.cell_set.calculate_foci(
self.parent.settings.foci_lookup_sensivity,
self.parent.settings.foci_area_fill_percent,
self.parent.settings.min_foci_radius,
self.parent.settings.max_foci_radius,
self.parent.settings.allowed_foci_overlap,
self.parent.settings.return_circles,
self.parent.settings.normalize_intensity,
(self.parent.settings.foci_rescale_min,
self.parent.settings.foci_rescale_max))
# Retrieving results
# self.cell_set.calculate_foci_parameters()
self.updateParamsTable()
self.parent.outfileButton.setEnabled(True)
self.parent.singleCellOutputBox.setEnabled(True)
for i in xrange(0, len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState(
) == QtCore.Qt.Checked:
self.imageDirs[i].write_all_pic_files(
self.parent.settings.nuclei_color,
self.parent.settings.foci_color)
#self.folderWidgets[i]=imageFolderWidget(imageDirPath)
# Table update
self.refreshImages()
self.updateAllImageLabels()
self.parent.pbar.setValue(100)
print("Foci calculation has finished for %s" % name)
def runCalc(self):
dir_path = self.fileMenuArea.getWorkDir()
dirs_with_images = self.fileMenuArea.getCheckedPaths()
if len(dirs_with_images) == 0:
return
else:
if (self.oldDirsWithImages == dirs_with_images) & self.lastCalc & (
not (self.settingsChanged)):
print "No changes in selection"
else:
pre_image_dirs = [image_dir for image_dir in dirs_with_images if \
(os.path.isfile(os.path.join(image_dir,self.nuclei_name)) and os.path.isfile(os.path.join(image_dir, self.foci_name)))]
image_dirs = [
pic_an.image_dir(image_dir, self.nuclei_name,
self.foci_name)
for image_dir in pre_image_dirs
]
name = unicode(QtCore.QDir(dir_path).dirName())
absoutfile = os.path.join(dir_path, unicode(self.outfile))
print absoutfile
cell_set = pic_an.cell_set(name=name, cells=[])
remained = len(image_dirs)
if remained != 0:
pbarval = 0
self.pbar.show()
self.pbar.setValue(pbarval)
pbarstep = (100 - 10) / remained
print "We have", remained, 'images to load for', name
print "Image loading have started for", name
for image_dir in image_dirs:
image_dir.load_separate_images(self.sensitivity,
self.min_cell_size)
pbarval += pbarstep
self.pbar.setValue(pbarval)
remained -= 1
if remained == 0:
print "Image loading have finished for", name
else:
print remained, 'images remained to load for', name
cell_set.extend(image_dir)
if len(cell_set.cells) == 0:
print "There are no cells in the images from ", dir_path
return
print "We have", len(
cell_set.cells), "cells to analyze for", name
cell_set.rescale_nuclei()
cell_set.rescale_foci(
(self.foci_rescale_min, self.foci_rescale_max))
self.oldFoci_rescale_min, self.oldFoci_rescale_max = cell_set.get_foci_rescale_values(
)
cell_set.calculate_foci(self.peak_min_val_perc,
self.foci_min_val_perc,
self.foci_radius,
self.foci_min_level_on_bg)
cell_set.calculate_foci_parameters()
cell_set.write_parameters(absoutfile)
params = cell_set.get_parameters()
self.statusArea.hide()
self.statusArea.setItem(
0, 0, QtGui.QTableWidgetItem(str(params[0])))
for i in xrange(1, 13):
self.statusArea.setItem(
(i + 1) % 2, (i + 1) // 2,
QtGui.QTableWidgetItem(str(params[i])))
#self.update()
for image_dir in image_dirs:
image_dir.write_all_pic_files(self.nuclei_color,
self.foci_color)
self.statusArea.show()
self.pbar.setValue(100)
self.updateImages()
self.fileMenuArea.updateWorkDir()
self.fileMenuArea.setCheckedFromPaths(dirs_with_images)
self.oldDirsWithImages = dirs_with_images
self.lastCalc = True
self.settingsChanged = False
else:
print "no images is dataset"
def getScale(self):
dir_path = self.fileMenuArea.getWorkDir()
dirs_with_images = self.fileMenuArea.getCheckedPaths()
if len(dirs_with_images) == 0:
return
else:
if (self.oldDirsWithImages
== dirs_with_images) & (not (self.settingsChanged)):
print "No changes in selection, setting values from previous calc"
self.foci_rescale_min = self.oldFoci_rescale_min
self.foci_rescale_max = self.oldFoci_rescale_max
print "Foci rescale min max", self.foci_rescale_min, self.foci_rescale_max
else:
### move to folderMenu widget?
pre_image_dirs = [image_dir for image_dir in dirs_with_images if \
(os.path.isfile(os.path.join(image_dir,self.nuclei_name)) and os.path.isfile(os.path.join(image_dir, self.foci_name)))]
image_dirs = [
pic_an.image_dir(image_dir, self.nuclei_name,
self.foci_name)
for image_dir in pre_image_dirs
]
#########################
name = unicode(QtCore.QDir(dir_path).dirName())
cell_set = pic_an.cell_set(name=name, cells=[])
remained = len(image_dirs)
if remained != 0:
pbarval = 0
self.pbar.show()
self.pbar.setValue(pbarval)
pbarstep = (100 - 10) / remained
print "We have", remained, 'images to load for', name
print "Image loading have started for", name
for image_dir in image_dirs:
image_dir.load_separate_images(self.sensitivity,
self.min_cell_size)
pbarval += pbarstep
self.pbar.setValue(pbarval)
remained -= 1
if remained == 0:
print "Image loading have finished for", name
else:
print remained, 'images remained to load for', name
cell_set.extend(image_dir)
if len(cell_set.cells) == 0:
print "There are no cells in the images from ", dir_path
return
print "We have", len(
cell_set.cells), "cells to analyze for", name
cell_set.rescale_foci((None, None))
self.foci_rescale_min, self.foci_rescale_max = cell_set.get_foci_rescale_values(
)
self.oldFoci_rescale_min, self.oldFoci_rescale_max = self.foci_rescale_min, self.foci_rescale_max
print "Foci rescale min max", self.foci_rescale_min, self.foci_rescale_max
self.pbar.setValue(100)
self.oldDirsWithImages = dirs_with_images
self.lastCalc = False
self.settingsChanged = False
else:
print "no images is dataset"
def openWorkDir(self,workdir=None):
if not(workdir):
workdir=QtGui.QFileDialog.getExistingDirectory(directory=self.workDir)
if workdir != "":
self.parent.workDir=unicode(workdir)
if workdir != "":
self.workDir=unicode(workdir)
for i in reversed(range(self.folderLayout.count())):
self.folderLayout.itemAt(i).widget().setParent(None)
self.selectedImage=""
self.selectedImageDir=""
self.checkedPaths=[]
self.nameList=[]
folderIterator=QtCore.QDirIterator(self.workDir,QtCore.QDir.Dirs|QtCore.QDir.NoDotAndDotDot)
while folderIterator.hasNext():
imageQDir=QtCore.QDir(folderIterator.next())
imageList= imageQDir.entryList(["*.TIF", "*.tif", "*.jpg", "*.JPG", "*.BMP", "*.bmp"])
for name in imageList:
if not(name in self.nameList):
self.nameList.append(unicode(name))
[self.parent.nuclNameComboBox.removeItem(0) for i in xrange(self.parent.nuclNameComboBox.count())]
self.parent.nuclNameComboBox.addItems(self.nameList)
if self.parent.settings.nuclei_name in self.nameList:
#print self.parent.nuclNameComboBox.itemText(1)
self.parent.nuclNameComboBox.setCurrentIndex(self.parent.nuclNameComboBox.findText(self.parent.settings.nuclei_name))
else:
self.parent.nuclNameComboBox.setCurrentIndex(0)
self.parent.settings.nuclei_name=self.nameList[0]
[self.parent.fociNameComboBox.removeItem(1) for i in xrange(1,self.parent.fociNameComboBox.count())]
self.parent.fociNameComboBox.addItems(self.nameList)
if self.parent.settings.foci_name in self.nameList:
self.parent.fociNameComboBox.setCurrentIndex(self.parent.fociNameComboBox.findText(self.parent.settings.foci_name))
else:
self.parent.fociNameComboBox.setCurrentIndex(0)
self.parent.settings.foci_name='--None--'
self.checkAllBox = QtGui.QCheckBox('Check/Uncheck All', self)
self.checkAllBox.setChecked(True)
self.checkAllBox.stateChanged.connect(lambda:
(self.checkAll() if self.checkAllBox.isChecked()
else self.unCheckAll()))
self.folderLayout.addWidget(self.checkAllBox)
self.folderWidgets=[]
self.imageDirs=[]
self.cell_set = pic_an.cell_set(name=self.workDir, cells=[])
i=0
folderIterator=QtCore.QDirIterator(self.workDir,QtCore.QDir.Dirs|QtCore.QDir.NoDotAndDotDot)
while folderIterator.hasNext():
imageQDir=QtCore.QDir(folderIterator.next())
nucleiPath=imageQDir.absolutePath() + QtCore.QDir.separator() + self.parent.settings.nuclei_name
fociPath=imageQDir.absolutePath() + QtCore.QDir.separator() + self.parent.settings.foci_name
if ((self.parent.settings.foci_name == '--None--')&(QtCore.QFile(nucleiPath).exists())):
self.imageDirs.append(pic_an.image_dir(unicode(imageQDir.absolutePath()),
unicode(self.parent.settings.nuclei_name)))
self.folderWidgets.append(imageFolderWidget(imageQDir))
self.folderLayout.addWidget(self.folderWidgets[-1])
self.folderWidgets[-1].signal_hideall.connect(self.hideAllImageLabels)
############
self.folderWidgets[-1].signal_show_image.connect(lambda key=i: self.updateImage(key))
self.folderWidgets[-1].signal_show_all_images.connect(lambda key=i: self.updateImages(key))
############
i+=1
elif ((QtCore.QFile(fociPath).exists())&(QtCore.QFile(nucleiPath).exists())):
self.imageDirs.append(pic_an.image_dir(unicode(imageQDir.absolutePath()),
unicode(self.parent.settings.nuclei_name),
unicode(self.parent.settings.foci_name)))
self.folderWidgets.append(imageFolderWidget(imageQDir))
self.folderLayout.addWidget(self.folderWidgets[-1])
self.folderWidgets[-1].signal_hideall.connect(self.hideAllImageLabels)
############
self.folderWidgets[-1].signal_show_image.connect(lambda key=i: self.updateImage(key))
self.folderWidgets[-1].signal_show_all_images.connect(lambda key=i: self.updateImages(key))
############
i+=1
print str(len(self.imageDirs)) + ' dirs found in working directory'
try:
self.updateImages(0)
except IndexError:
self.signal_update_images.emit()
def calculateSelected(self):
self.parent.outfileButton.setEnabled(False)
self.parent.singleCellOutputBox.setEnabled(False)
name=QtCore.QDir(self.workDir).dirName()
self.cell_set = pic_an.cell_set(name=name, cells=[])
tasksize=len(self.getCheckedPaths())
print("We have %d images to load for %s" % (tasksize, name))
self.parent.pbar.show()
pbarvalue=0
self.parent.pbar.setValue(pbarvalue)
pbarstep = (100 - 10 )/ tasksize
# Calculation
if len(self.folderWidgets) != 0:
if self.parent.settings.foci_name == '--None--':
for i in xrange(0,len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState() == QtCore.Qt.Checked :
self.imageDirs[i].detect_cells(self.parent.settings.sensitivity,
self.parent.settings.min_cell_size, load_foci=False)
self.cell_set.extend(self.imageDirs[i])
tasksize -= 1
if tasksize == 0:
print("Image loading has finished for %s" % name)
else:
print('%d images remained to load for %s' % (tasksize, name))
pbarvalue+=pbarstep
self.parent.pbar.setValue(pbarvalue)
for i in xrange(0,len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState() == QtCore.Qt.Checked :
self.imageDirs[i].write_all_pic_files(self.parent.settings.nuclei_color,
self.parent.settings.foci_color)
self.updateParamsTable()
self.updateAllImageLabels()
self.refreshImages()
self.parent.pbar.setValue(100)
self.parent.outfileButton.setEnabled(True)
self.parent.singleCellOutputBox.setEnabled(True)
else:
for i in xrange(0,len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState() == QtCore.Qt.Checked :
self.imageDirs[i].detect_cells(self.parent.settings.sensitivity,
self.parent.settings.min_cell_size, load_foci=True)
self.cell_set.extend(self.imageDirs[i])
tasksize -= 1
if tasksize == 0:
print("Image loading has finished for %s" % name)
else:
print('%d images remained to load for %s' % (tasksize, name))
pbarvalue+=pbarstep
self.parent.pbar.setValue(pbarvalue)
if len(self.cell_set.cells) == 0:
print("No cells were detected in %s" % name)
return
print("We have %d cells to analyze for %s" % (len(self.cell_set.cells), name))
self.cell_set.calculate_foci(self.parent.settings.foci_lookup_sensivity,
self.parent.settings.foci_area_fill_percent,
self.parent.settings.min_foci_radius,
self.parent.settings.max_foci_radius,
self.parent.settings.allowed_foci_overlap,
self.parent.settings.return_circles,
self.parent.settings.normalize_intensity,
(self.parent.settings.foci_rescale_min,
self.parent.settings.foci_rescale_max))
# Retrieving results
# self.cell_set.calculate_foci_parameters()
self.updateParamsTable()
self.parent.outfileButton.setEnabled(True)
self.parent.singleCellOutputBox.setEnabled(True)
for i in xrange(0,len(self.folderWidgets)):
if self.folderWidgets[i].checked.checkState() == QtCore.Qt.Checked :
self.imageDirs[i].write_all_pic_files(self.parent.settings.nuclei_color,
self.parent.settings.foci_color)
#self.folderWidgets[i]=imageFolderWidget(imageDirPath)
# Table update
self.refreshImages()
self.updateAllImageLabels()
self.parent.pbar.setValue(100)
print("Foci calculation has finished for %s" % name)
