def __init__(self, mainWindow=None, histologyAnalyser=None):
self.mainWindow = mainWindow
self.ha = histologyAnalyser
self.hr = HistologyReport()
self.hr.data = self.ha.stats
self.hr.generateStats()
QDialog.__init__(self)
self.initUI()
self.mainWindow.setStatusBarText('Finished')
def processData(args):
"""
Processing data without gui
"""
inputfile=args.inputfile
threshold=args.threshold
mask_file=args.maskfile
crop=args.crop
voxelsize=args.voxelsize
binaryClosing=args.binaryopening
binaryOpening=args.binaryclosing
# Reading/Generating data
if inputfile is None: # # Using generated sample data
logger.info('Generating sample data...')
metadata = {'voxelsize_mm': [1, 1, 1]}
data3d = generate_sample_data(1, 0, 0)
else: # Normal runtime
dr = datareader.DataReader()
data3d, metadata = dr.Get3DData(inputfile)
# Custom voxel size
if voxelsize is not None:
metadata['voxelsize_mm'] = voxelsize
# Crop data
if crop is not None:
logger.debug('Croping data: %s', str(crop))
data3d = data3d[crop[0]:crop[1], crop[2]:crop[3], crop[4]:crop[5]].copy()
# Init HistologyAnalyser object
logger.debug('Init HistologyAnalyser object')
ha = HistologyAnalyser(data3d, metadata, threshold,
binaryClosing=binaryClosing, binaryOpening=binaryOpening,
nogui=True)
# Remove Area = Load mask from file
if mask_file is not None:
logger.debug('Loading mask from file...')
mask = misc.obj_from_file(filename=mask_file, filetype='pickle')
if ha.data3d.shape == mask.shape:
ha.data3d_masked = mask
ha.data3d[mask == 0] = np.min(ha.data3d)
else:
raise ValueError('Mask file has wrong dimensions '+str(mask.shape))
# Segmentation
logger.debug('Segmentation')
ha.data_to_skeleton()
# Computing statistics
logger.info("# ## ## ## ## statistics")
ha.data_to_statistics()
# Saving files
logger.info("# ## ## write stats to file")
ha.writeStatsToCSV()
ha.writeStatsToYAML()
# ## Histology report
logger.info("# ## ## Histology report")
hr = HistologyReport()
hr.data = ha.stats
hr.generateStats()
hr.writeReportToCSV()
hr.writeReportToYAML()
# Add results Record
if crop is not None:
label = str(crop[0])+"-"+str(crop[1])
else:
label = "0-end"
if inputfile is None:
hr.addResultsRecord(label=label)
else:
hr.addResultsRecord(label=label, datapath=inputfile)
# ## End
logger.info('Finished')
class StatsResultDialog(QDialog):
def __init__(self, mainWindow=None, histologyAnalyser=None):
self.mainWindow = mainWindow
self.ha = histologyAnalyser
self.hr = HistologyReport()
self.hr.data = self.ha.stats
self.hr.generateStats()
QDialog.__init__(self)
self.initUI()
self.mainWindow.setStatusBarText('Finished')
def initUI(self):
self.ui_gridLayout = QGridLayout()
self.ui_gridLayout.setSpacing(15)
rstart = 0
font_info = QFont()
font_info.setBold(True)
font_info.setPixelSize(20)
label = QLabel('Finished')
label.setFont(font_info)
self.ui_gridLayout.addWidget(label, rstart + 0, 0, 1, 1)
rstart +=1
### histology report
report = self.hr.stats['Report']
report_label = QLabel('Total length mm: '+str(report['Total length mm'])+'\n'
+'Avg length mm: '+str(report['Avg length mm'])+'\n'
+'Avg radius mm: '+str(report['Avg radius mm'])
)
histogram_radius = HistogramMplCanvas(report['Radius histogram'][0],
report['Radius histogram'][1],
title='Radius histogram',
xlabel="Blood-vessel radius [mm]",
ylabel="Number"
)
histogram_length = HistogramMplCanvas(report['Length histogram'][0],
report['Length histogram'][1],
title='Length histogram',
xlabel="Blood-vessel length [mm]",
ylabel="Number"
)
self.ui_gridLayout.addWidget(report_label, rstart + 0, 0, 1, 3)
self.ui_gridLayout.addWidget(histogram_radius, rstart + 1, 0, 1, 3)
self.ui_gridLayout.addWidget(histogram_length, rstart + 2, 0, 1, 3)
rstart +=3
### buttons
btn_yaml = QPushButton("Write statistics to YAML", self)
btn_yaml.clicked.connect(self.writeYAML)
btn_csv = QPushButton("Write statistics to CSV", self)
btn_csv.clicked.connect(self.writeCSV)
btn_rep_yaml = QPushButton("Write report to YAML", self)
btn_rep_yaml.clicked.connect(self.writeReportYAML)
btn_rep_csv = QPushButton("Write report to CSV", self)
btn_rep_csv.clicked.connect(self.writeReportCSV)
self.ui_gridLayout.addWidget(btn_yaml, rstart + 0, 0)
self.ui_gridLayout.addWidget(btn_csv, rstart + 0, 1)
self.ui_gridLayout.addWidget(btn_rep_yaml, rstart + 1, 0)
self.ui_gridLayout.addWidget(btn_rep_csv, rstart + 1, 1)
rstart +=2
### Stretcher
self.ui_gridLayout.addItem(QSpacerItem(0,0), rstart + 0, 0,)
self.ui_gridLayout.setRowStretch(rstart + 0, 1)
rstart +=1
### Setup layout
self.setLayout(self.ui_gridLayout)
self.show()
def writeYAML(self):
# TODO - choose save path
logger.info("Writing statistics YAML file")
self.mainWindow.setStatusBarText('Statistics - writing YAML file')
self.ha.writeStatsToYAML()
self.mainWindow.setStatusBarText('Ready')
def writeCSV(self):
# TODO - choose save path
logger.info("Writing statistics CSV file")
self.mainWindow.setStatusBarText('Statistics - writing CSV file')
self.ha.writeStatsToCSV()
self.mainWindow.setStatusBarText('Ready')
def writeReportYAML(self):
# TODO - choose save path
logger.info("Writing report YAML file")
self.mainWindow.setStatusBarText('Report - writing YAML file')
self.hr.writeReportToYAML()
self.mainWindow.setStatusBarText('Ready')
def writeReportCSV(self):
# TODO - choose save path
logger.info("Writing report CSV file")
self.mainWindow.setStatusBarText('Report - writing CSV file')
self.hr.writeReportToCSV()
self.mainWindow.setStatusBarText('Ready')
def test_synthetic_data_vessel_tree_evaluation(self):
"""
Generovani umeleho stromu do 3D a jeho evaluace.
V testu dochazi ke kontrole predpokladaneho objemu a deky cev
"""
from gen_volume_tree import TreeVolumeGenerator
from histology_analyser import HistologyAnalyser
from histology_report import HistologyReport
import segmentation
import misc
# generate 3d data from yaml for testing
tvg = TreeVolumeGenerator()
yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
tvg.importFromYaml(yaml_path)
tvg.voxelsize_mm = [1,1,1]
tvg.shape = [100,100,100]
tvg.generateTree()
# init histology Analyser
metadata = {'voxelsize_mm': tvg.voxelsize_mm}
data3d = tvg.data3d*10
threshold = 2.5
ha = HistologyAnalyser(data3d, metadata, threshold)
# modifited ha.data_to_skeleton() function
data3d_thr = segmentation.vesselSegmentation(
data3d,
segmentation=np.ones(tvg.data3d.shape, dtype='int8'),
threshold=threshold,
inputSigma=0.15,
dilationIterations=2,
nObj=1,
biggestObjects=False,
interactivity=False,
binaryClosingIterations=5,
binaryOpeningIterations=1)
data3d_skel = ha.binar_to_skeleton(data3d_thr)
# get statistics
ha.skeleton_to_statistics(data3d_thr, data3d_skel)
yaml_new = "hist_stats_new.yaml"
ha.writeStatsToYAML(filename=yaml_new)
# get histology reports
hr = HistologyReport()
hr.importFromYaml(yaml_path)
hr.generateStats()
stats_orig = hr.stats
hr = HistologyReport()
hr.importFromYaml(os.path.join(path_to_script, yaml_new))
hr.generateStats()
stats_new = hr.stats
# compare
self.assertGreater(stats_orig['Total length mm'],stats_new['Total length mm']*0.9)
self.assertLess(stats_orig['Total length mm'],stats_new['Total length mm']*1.1)
self.assertGreater(stats_orig['Avg length mm'],stats_new['Avg length mm']*0.9)
self.assertLess(stats_orig['Avg length mm'],stats_new['Avg length mm']*1.1)
self.assertGreater(stats_orig['Avg radius mm'],stats_new['Avg radius mm']*0.9)
self.assertLess(stats_orig['Avg radius mm'],stats_new['Avg radius mm']*1.1)
