def __init__(self, settings_filename=None, settings=None, tissue_id=None):
if settings is None and settings_filename is None:
raise ValueError(
"Either a settings object or a settings filename has to be given."
)
if not settings is None:
self.settings = settings
elif not settings_filename is None:
self.settings = Settings(os.path.abspath(settings_filename),
dctGlobals=globals())
if not tissue_id is None:
print('Overwriting settings ... ')
self.settings = overwrite_settings(self.settings, tissue_id)
print('tissue id: %s' % tissue_id)
print('output_folder: %s' % self.settings.output_folder)
for folder in self.settings.makefolders:
if not os.path.exists(folder):
os.makedirs(folder)
self.cluster_folder = os.path.join(self.settings.output_folder,
'clustering')
self.plot_projection_folder = os.path.join(self.settings.output_folder,
'projections')
for folder in [self.cluster_folder, self.plot_projection_folder]:
if not os.path.isdir(folder):
os.makedirs(folder)
self.sp = SpotDetector(settings=self.settings)
self.cell_detector = CellDetection(settings=self.settings)
self.ilastik = Ilastik(settings=self.settings)
self.markers = self.settings.cluster_markers[self.settings.dataset]
self.nb_clusters = 60
def __init__(self, settings_filename=None, settings=None, tissue_id=None):
if settings is None and settings_filename is None:
raise ValueError(
"Either a settings object or a settings filename has to be given."
)
if not settings is None:
self.settings = settings
elif not settings_filename is None:
self.settings = Settings(os.path.abspath(settings_filename),
dctGlobals=globals())
if not tissue_id is None:
print('Overwriting settings ... ')
self.settings = overwrite_settings(self.settings, tissue_id)
print('tissue id: %s' % tissue_id)
print('output_folder: %s' % self.settings.output_folder)
for folder in self.settings.makefolders:
if not os.path.exists(folder):
os.makedirs(folder)
self.cluster_folder = os.path.join(self.settings.output_folder,
'clustering')
self.plot_projection_folder = os.path.join(self.settings.output_folder,
'projections')
for folder in [self.cluster_folder, self.plot_projection_folder]:
if not os.path.isdir(folder):
os.makedirs(folder)
self.sp = SpotDetector(settings=self.settings)
self.fissure = FissureDetection(settings=self.settings)
self.cell_detector = CellDetection(settings=self.settings)
self.ilastik = Ilastik(settings=self.settings)
# all markers except for empty,
self.all_markers = [
'CD206', 'IL-21', 'CD185(CXCR5)', 'CD45', 'CXCL13',
'CD1c-biotin-NA', 'CD303(BDCA2)', 'CD11b', 'Bcl-6', 'CD45RA',
'E-Cadherin', 'CD141', 'CD123', 'CD68', 'CD279(PD-1)', 'HLA-DR',
'aSMA', 'CD370', 'CD11c', 'CD19', 'ICOS', 'CD56(NCAM)', 'CD3',
'CD14'
]
self.acceptable_markers = [
'E-Cadherin', 'aSMA', 'CD45', 'IL-21', 'CXCL13', 'CD279(PD-1)',
'CD3', 'CD45RA', 'Bcl-6', 'CD19', 'HLA-DR', 'CD11c', 'CD14',
'CD68', 'CD206', 'CD370', 'CD141', 'CD123'
]
self.markers = self.settings.cluster_markers[self.settings.dataset]
self.nb_clusters = 60
def __init__(self, settings_filename=None, settings=None,
tissue_id=None):
if settings is None and settings_filename is None:
raise ValueError("Either a settings object or a settings filename has to be given.")
if not settings is None:
self.settings = settings
elif not settings_filename is None:
self.settings = Settings(os.path.abspath(settings_filename), dctGlobals=globals())
if not tissue_id is None:
print('Overwriting settings ... ')
self.settings = overwrite_settings(self.settings, tissue_id)
print('tissue id: %s' % tissue_id)
print('output_folder: %s' % self.settings.output_folder)
for folder in self.settings.makefolders:
if not os.path.exists(folder):
os.makedirs(folder)
def __init__(self, settings_filename=None, settings=None, tissue_id=None):
if settings is None and settings_filename is None:
raise ValueError("Either a settings object or a settings filename has to be given.")
if not settings is None:
self.settings = settings
elif not settings_filename is None:
self.settings = Settings(os.path.abspath(settings_filename), dctGlobals=globals())
for folder in self.settings.makefolders:
if not os.path.exists(folder):
os.makedirs(folder)
if not tissue_id is None:
print('Overwriting settings ... ')
self.settings = overwrite_settings(self.settings, tissue_id)
print('tissue id: %s' % tissue_id)
print('output_folder: %s' % self.settings.output_folder)
self.sp = SpotDetector(settings=self.settings)
self.fissure = FissureDetection(settings=self.settings)
self.image_result_folder = os.path.join(self.settings.output_folder,
'cell_segmentation')
if not os.path.isdir(self.image_result_folder):
os.makedirs(self.image_result_folder)