def _process_image(self, ):
self.image_viewer.remove_objects()
settings = BaseProcessorFrame.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('skip_finished', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('Processing')
_classify_objects = self._show_objects_by == 'classification'
settings.set2('primary_classification', _classify_objects)
settings.set2('secondary_classification', _classify_objects)
settings.set2('tertiary_classification', _classify_objects)
settings.set2('merged_classification', _classify_objects)
settings.set2('primary_featureextraction', _classify_objects)
settings.set2('secondary_featureextraction', _classify_objects)
settings.set2('objectdetection', self._detect_objects)
settings.set2('tracking', False)
settings.set('Output', 'hdf5_create_file', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the same color
if nchannels == 2:
settings.set('General', 'process_secondary', True)
elif nchannels >= 3:
settings.set('General', 'process_secondary', True)
settings.set('General', 'process_tertiary', True)
settings.set('General', 'rendering', {})
analyzer = AnalyzerBrowser(self.coordinate.plate, settings,
self._imagecontainer)
res = None
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
res = analyzer()
self.render_browser(res)
except Exception, e:
import traceback
traceback.print_exc()
QMessageBox.critical(self, "Error", str(e))
raise
def _process_image(self, ):
self.image_viewer.remove_objects()
settings = BaseProcessorFrame.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('skip_finished', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('Processing')
_classify_objects = self._show_objects_by == 'classification'
settings.set2('primary_classification', _classify_objects )
settings.set2('secondary_classification', _classify_objects)
settings.set2('tertiary_classification', _classify_objects)
settings.set2('merged_classification', _classify_objects)
settings.set2('primary_featureextraction', _classify_objects)
settings.set2('secondary_featureextraction', _classify_objects)
settings.set2('objectdetection', self._detect_objects)
settings.set2('tracking', False)
settings.set('Output', 'hdf5_create_file', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the same color
if nchannels == 2:
settings.set('General', 'process_secondary', True)
elif nchannels >= 3:
settings.set('General', 'process_secondary', True)
settings.set('General', 'process_tertiary', True)
settings.set('General', 'rendering', {})
analyzer = AnalyzerBrowser(self.coordinate.plate, settings, self._imagecontainer)
res = None
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
res = analyzer()
self.render_browser(res)
except Exception, e:
import traceback
traceback.print_exc()
QMessageBox.critical(self, "Error", str(e))
raise
def get_export_settings(self, settings, has_timelapse=True):
settings = BaseProcessorFrame.get_special_settings(
settings, has_timelapse)
settings.set('General', 'version', version)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
# set properties of merged channel to the same as for Primary
for prefix in CH_PRIMARY + CH_OTHER:
if prefix == CH_PRIMARY[0] \
or settings.get('General', 'process_%s' %prefix):
d = {} # render settings for contours
for x in self.plugin_mgr.region_info.names[prefix]:
d = {
'%s_contours_%s' % (prefix, x): {
prefix.capitalize(): {
'raw': ('#FFFFFF', 1.0),
'contours':
[(x, self.plugin_mgr.region_info.colors[x], 1,
False)]
}
}
}
settings.get('General', 'rendering').update(d)
# render settings for classifications
d = {}
if (settings.get('General', 'process_%s' %prefix) and \
settings.get('Processing', '%s_classification' % prefix)):
for x in self.plugin_mgr.region_info.names[prefix]:
if x == settings.get('Classification', '%s_classification_regionname' % prefix) or \
prefix == CH_VIRTUAL[0]:
d = {
'%s_classification_%s' % (prefix, x): {
prefix.capitalize(): {
'raw': ('#FFFFFF', 1.0),
'contours': [(x, 'class_label', 1, False),
(x, '#000000', 1, False)]
}
}
}
if settings('EventSelection', 'supervised_event_selection'):
settings.get('General', 'rendering_class').update(d)
# setup rendering properties for merged channel
# want the same rendering properties as for the primary channel!
if settings.get('General', 'process_merged'):
# color are defined for regions (not for channels)
# therefore, we first retrieve the regions for the primary channel
# and (in the case there are some) we assign the color of the first
# ROI of the primary channel to the merged contour.
regions_primary = self.plugin_mgr.region_info.names[CH_PRIMARY[0]]
if len(regions_primary) == 0:
default_color = '#FF00FF'
else:
default_color = self.plugin_mgr.region_info.colors[
regions_primary[0]]
regions = self._merged_regions(settings)
d = {
'merged_contours_%s' % str(regions): {
"Merged": {
'raw': ('#FFFFFF', 1.0),
'contours': [(regions, default_color, 1, False)]
}
}
}
settings.get("General", "rendering").update(d)
if settings.get('Processing', 'merged_classification'):
d = {
'merged_classification_%s' % str(regions): {
"Merged": {
'raw': ('#FFFFFF', 1.0),
'contours': [(regions, 'class_label', 1, False),
(regions, '#000000', 1, False)]
}
}
}
settings.get("General", "rendering_class").update(d)
return settings
def get_export_settings(self, settings, has_timelapse=True):
settings = BaseProcessorFrame.get_special_settings(settings, has_timelapse)
settings.set('General', 'version', version)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
show_ids = settings.get('Output', 'rendering_contours_showids')
show_ids_class = settings.get('Output', 'rendering_class_showids')
# set properties of merged channel to the same as for Primary
for prefix in CH_PRIMARY+CH_OTHER:
if prefix == CH_PRIMARY[0] \
or settings.get('General', 'process_%s' %prefix):
d = {} # render settings for contours
for x in self.plugin_mgr.region_info.names[prefix]:
d = {'%s_contours_%s' % (prefix, x):
{prefix.capitalize(): {'raw': ('#FFFFFF', 1.0),
'contours': [(x, self.plugin_mgr.region_info.colors[x], 1, show_ids)]
}
}
}
settings.get('General', 'rendering').update(d)
# render settings for classifications
d = {}
if (settings.get('General', 'process_%s' %prefix) and \
settings.get('Processing', '%s_classification' % prefix)):
for x in self.plugin_mgr.region_info.names[prefix]:
if x == settings.get('Classification', '%s_classification_regionname' % prefix) or \
prefix == CH_VIRTUAL[0]:
d = {'%s_classification_%s' % (prefix, x):
{prefix.capitalize(): {'raw': ('#FFFFFF', 1.0),
'contours': [(x, 'class_label', 1, False),
(x, '#000000' , 1, show_ids_class)]
}
}
}
if settings('EventSelection', 'supervised_event_selection'):
settings.get('General', 'rendering_class').update(d)
# setup rendering properties for merged channel
# want the same rendering properties as for the primary channel!
if settings.get('General', 'process_merged'):
# color are defined for regions (not for channels)
# therefore, we first retrieve the regions for the primary channel
# and (in the case there are some) we assign the color of the first
# ROI of the primary channel to the merged contour.
regions_primary = self.plugin_mgr.region_info.names[CH_PRIMARY[0]]
if len(regions_primary) == 0:
default_color = '#FF00FF'
else:
default_color = self.plugin_mgr.region_info.colors[regions_primary[0]]
regions = self._merged_regions(settings)
d = {'merged_contours_%s' %str(regions):
{"Merged": {'raw': ('#FFFFFF', 1.0),
'contours': [(regions, default_color, 1, show_ids)]}}}
settings.get("General", "rendering").update(d)
if settings.get('Processing', 'merged_classification'):
d = {'merged_classification_%s' %str(regions):
{"Merged": {'raw': ('#FFFFFF', 1.0),
'contours': [(regions, 'class_label', 1, False),
(regions, '#000000' , 1, show_ids_class)]}}}
settings.get("General", "rendering_class").update(d)
if has_timelapse:
# generate raw images of selected channels (later used for gallery images)
if settings.get('Output', 'events_export_gallery_images'):
for prefix in CHANNEL_PREFIX:
if prefix == 'primary' or settings.get('General', 'process_%s' % prefix):
settings.get('General', 'rendering').update({prefix : {prefix.capitalize() :
{'raw': ('#FFFFFF', 1.0)}}})
return settings
def get_export_settings(cls, settings, has_timelapse=True):
settings = BaseProcessorFrame.get_special_settings(
settings, has_timelapse)
settings.set('General', 'version', VERSION)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
show_ids = settings.get('Output', 'rendering_contours_showids')
show_ids_class = settings.get('Output', 'rendering_class_showids')
# set propertys of merged channel to the same as for Primary
# unfortunately REGION_INFO is like a global variable
d = {}
for prefix in CH_PRIMARY + CH_OTHER:
if prefix == CH_PRIMARY[0] \
or settings.get('Processing', '%s_processchannel' % prefix):
for x in reginfo.names[prefix]:
d = {
'%s_contours_%s' % (prefix, x): {
prefix.capitalize(): {
'raw': ('#FFFFFF', 1.0),
'contours':
[(x, reginfo.colors[x], 1, show_ids)]
}
}
}
settings.get('General', 'rendering').update(d)
if settings.get('Processing', '%s_classification' % prefix):
for x in reginfo.names[prefix]:
if x == settings.get('Classification', '%s_classification_regionname' % prefix) or \
prefix == CH_VIRTUAL[0]:
d = {
'%s_classification_%s' % (prefix, x): {
prefix.capitalize(): {
'raw': ('#FFFFFF', 1.0),
'contours':
[(x, 'class_label', 1, False),
(x, '#000000', 1, show_ids_class)]
}
}
}
settings.get('General', 'rendering_class').update(d)
# setup rendering properties for merged channel
# want the same rendering properties as for the primary channel!
if settings.get('Processing', 'merged_processchannel'):
regions = cls._merged_regions(settings)
d = {
'merged_contours_%s' % '-'.join(regions): {
"Merged": {
'raw': ('#FFFFFF', 1.0),
'contours':
[(regions, reginfo.colors["primary"], 1, show_ids)]
}
}
}
settings.get("General", "rendering").update(d)
if settings.get('Processing', 'merged_classification'):
d = {
'merged_classification_%s' % '-'.join(regions): {
"Merged": {
'raw': ('#FFFFFF', 1.0),
'contours':
[(regions, 'class_label', 1, False),
(regions, '#000000', 1, show_ids_class)]
}
}
}
settings.get("General", "rendering_class").update(d)
if has_timelapse:
# generate raw images of selected channels (later used for gallery images)
if settings.get('Output', 'events_export_gallery_images'):
for prefix in CHANNEL_PREFIX:
if prefix == 'primary' or settings.get(
'Processing', '%s_processchannel' % prefix):
settings.get('General', 'rendering').update({
prefix: {
prefix.capitalize(): {
'raw': ('#FFFFFF', 1.0)
}
}
})
return settings
def _process_image(self, ):
self.image_viewer.remove_objects()
settings = BaseProcessorFrame.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('redofailedonly', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('Processing')
_classify_objects = self._show_objects_by == 'classification'
settings.set2('primary_classification', _classify_objects )
settings.set2('secondary_classification', _classify_objects)
settings.set2('tertiary_classification', _classify_objects)
settings.set2('merged_classification', _classify_objects)
settings.set2('primary_featureextraction', _classify_objects)
settings.set2('secondary_featureextraction', _classify_objects)
settings.set2('objectdetection', self._detect_objects)
settings.set2('tracking', False)
settings.set_section('Output')
settings.set2('rendering_contours_discwrite', False)
settings.set2('rendering_class_discwrite', False)
settings.set2('export_object_counts', False)
settings.set2('export_object_details', False)
settings.set2('export_track_data', False)
settings.set2('hdf5_create_file', False)
settings.set_section('Classification')
settings.set2('collectsamples', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
settings.set('Output', 'events_export_gallery_images', False)
# turn of output:
settings.set('Output', 'export_object_counts', False)
settings.set('Output', 'export_object_details', False)
settings.set('Output', 'export_file_names', False)
settings.set('Output', 'events_export_gallery_images', False)
settings.set('Output', 'export_track_data', False)
settings.set('Output', 'export_tracking_as_dot', False)
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the same color
if nchannels == 2:
settings.set('General', 'process_secondary', True)
elif nchannels >= 3:
settings.set('General', 'process_secondary', True)
settings.set('General', 'process_tertiary', True)
settings.set('General', 'rendering', {})
analyzer = AnalyzerBrowser(self.coordinate.plate,
settings,
self._imagecontainer)
res = None
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
res = analyzer.processPositions()
self.render_browser(res)
except Exception, e:
import traceback
from cecog.gui.util import exception
traceback.print_exc()
exception(self, str(e))
raise
def get_export_settings(cls, settings, has_timelapse=True):
settings = BaseProcessorFrame.get_special_settings(settings, has_timelapse)
settings.set('General', 'version', VERSION)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
show_ids = settings.get('Output', 'rendering_contours_showids')
show_ids_class = settings.get('Output', 'rendering_class_showids')
# set propertys of merged channel to the same as for Primary
# unfortunately REGION_INFO is like a global variable
d = {}
for prefix in CH_PRIMARY+CH_OTHER:
if prefix == CH_PRIMARY[0] \
or settings.get('Processing', '%s_processchannel' % prefix):
for x in reginfo.names[prefix]:
d = {'%s_contours_%s' % (prefix, x):
{prefix.capitalize(): {'raw': ('#FFFFFF', 1.0),
'contours': [(x, reginfo.colors[x], 1, show_ids)]
}
}
}
settings.get('General', 'rendering').update(d)
if settings.get('Processing', '%s_classification' % prefix):
for x in reginfo.names[prefix]:
if x == settings.get('Classification', '%s_classification_regionname' % prefix) or \
prefix == CH_VIRTUAL[0]:
d = {'%s_classification_%s' % (prefix, x):
{prefix.capitalize(): {'raw': ('#FFFFFF', 1.0),
'contours': [(x, 'class_label', 1, False),
(x, '#000000' , 1, show_ids_class)]
}
}
}
settings.get('General', 'rendering_class').update(d)
# setup rendering properties for merged channel
# want the same rendering properties as for the primary channel!
if settings.get('Processing', 'merged_processchannel'):
regions = cls._merged_regions(settings)
d = {'merged_contours_%s' %'-'.join(regions):
{"Merged": {'raw': ('#FFFFFF', 1.0),
'contours': [(regions, reginfo.colors["primary"], 1, show_ids)]}}}
settings.get("General", "rendering").update(d)
if settings.get('Processing', 'merged_classification'):
d = {'merged_classification_%s' %'-'.join(regions):
{"Merged": {'raw': ('#FFFFFF', 1.0),
'contours': [(regions, 'class_label', 1, False),
(regions, '#000000' , 1, show_ids_class)]}}}
settings.get("General", "rendering_class").update(d)
if has_timelapse:
# generate raw images of selected channels (later used for gallery images)
if settings.get('Output', 'events_export_gallery_images'):
for prefix in CHANNEL_PREFIX:
if prefix == 'primary' or settings.get('Processing', '%s_processchannel' % prefix):
settings.get('General', 'rendering').update({prefix : {prefix.capitalize() :
{'raw': ('#FFFFFF', 1.0)}}})
return settings
def get_export_settings(cls, settings, has_timelapse=True):
settings = BaseProcessorFrame.get_special_settings(settings, has_timelapse)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
additional_prefixes = [SecondaryChannel.PREFIX, TertiaryChannel.PREFIX]
settings.set_section('Classification')
sec_class_regions = dict([(prefix,
settings.get2('%s_classification_regionname' % prefix))
for prefix in additional_prefixes])
settings.set_section('ObjectDetection')
prim_id = PrimaryChannel.NAME
sec_ids = dict([(x.PREFIX, x.NAME) for x in [SecondaryChannel, TertiaryChannel]])
sec_regions = dict([(prefix, [v for k,v in regions.iteritems() if settings.get2(k)])
for prefix, regions in [(SecondaryChannel.PREFIX, SECONDARY_REGIONS),
(TertiaryChannel.PREFIX, TERTIARY_REGIONS),
]
])
show_ids = settings.get('Output', 'rendering_contours_showids')
show_ids_class = settings.get('Output', 'rendering_class_showids')
settings.get('General', 'rendering').update({'primary_contours': {prim_id: {'raw': ('#FFFFFF', 1.0),
'contours': {'primary': ('#FF0000', 1, show_ids)}}}})
settings.set_section('Processing')
if settings.get2('primary_classification'):
settings.get('General', 'rendering_class').update({'primary_classification': {prim_id: {'raw': ('#FFFFFF', 1.0),
'contours': [('primary', 'class_label', 1, False),
('primary', '#000000', 1, show_ids_class),
]}}})
for prefix in additional_prefixes:
if settings.get2('%s_processchannel' % prefix):
sec_id = sec_ids[prefix]
settings.get('General', 'rendering').update(dict([('%s_contours_%s' % (prefix, x), {sec_id: {'raw': ('#FFFFFF', 1.0),
'contours': [(x, SECONDARY_COLORS[x] , 1, show_ids)]
}})
for x in sec_regions[prefix]]))
if settings.get2('%s_classification' % prefix):
sec_id = sec_ids[prefix]
sec_region = sec_class_regions[prefix]
settings.get('General', 'rendering_class').update({'%s_classification_%s' % (prefix, sec_region):
{sec_id: {'raw': ('#FFFFFF', 1.0),
'contours': [(sec_region, 'class_label', 1, False),
(sec_region, '#000000', 1, show_ids_class),
]}}})
if has_timelapse:
# generate raw images of selected channels (later used for gallery images)
if settings.get('Output', 'events_export_gallery_images'):
settings.get('General', 'rendering').update({'primary' : {prim_id : {'raw': ('#FFFFFF', 1.0)}}})
for prefix in additional_prefixes:
if settings.get2('%s_processchannel' % prefix):
sec_id = sec_ids[prefix]
settings.get('General', 'rendering').update({prefix : {sec_id : {'raw': ('#FFFFFF', 1.0)}}})
return settings
def _process_image(self, ):
self.image_viewer.remove_objects()
settings = BaseProcessorFrame.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('redofailedonly', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('Processing')
_classify_objects = self._show_objects_by == 'classification'
settings.set2('primary_classification', _classify_objects)
settings.set2('secondary_classification', _classify_objects)
settings.set2('tertiary_classification', _classify_objects)
settings.set2('merged_classification', _classify_objects)
settings.set2('primary_featureextraction', _classify_objects)
settings.set2('secondary_featureextraction', _classify_objects)
settings.set2('objectdetection', self._detect_objects)
settings.set2('tracking', False)
settings.set_section('Output')
settings.set2('rendering_contours_discwrite', False)
settings.set2('rendering_class_discwrite', False)
settings.set2('export_object_counts', False)
settings.set2('export_object_details', False)
settings.set2('export_track_data', False)
settings.set2('hdf5_create_file', False)
settings.set_section('Classification')
settings.set2('collectsamples', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
settings.set('Output', 'events_export_gallery_images', False)
# turn of output:
settings.set('Output', 'export_object_counts', False)
settings.set('Output', 'export_object_details', False)
settings.set('Output', 'export_file_names', False)
settings.set('Output', 'events_export_gallery_images', False)
settings.set('Output', 'export_track_data', False)
settings.set('Output', 'export_tracking_as_dot', False)
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the same color
if nchannels == 2:
settings.set('General', 'process_secondary', True)
elif nchannels >= 3:
settings.set('General', 'process_secondary', True)
settings.set('General', 'process_tertiary', True)
settings.set('General', 'rendering', {})
analyzer = AnalyzerBrowser(self.coordinate.plate, settings,
self._imagecontainer)
res = None
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
res = analyzer.processPositions()
self.render_browser(res)
except Exception, e:
import traceback
from cecog.gui.util import exception
traceback.print_exc()
exception(self, str(e))
raise