def get_measurement_columns(self, pipeline):
'''Return column definitions for measurements made by this module'''
columns = cpmi.get_object_measurement_columns(self.objects_name.value)
columns += [(self.primary_objects.value,
cpmi.FF_CHILDREN_COUNT % self.objects_name.value,
cpmeas.COLTYPE_INTEGER),
(self.objects_name.value,
cpmi.FF_PARENT % self.primary_objects.value,
cpmeas.COLTYPE_INTEGER)]
if self.method != M_DISTANCE_N:
columns += cpmi.get_threshold_measurement_columns(
self.objects_name.value)
if self.wants_discard_edge and self.wants_discard_primary:
columns += cpmi.get_object_measurement_columns(
self.new_primary_objects_name.value)
columns += [(self.new_primary_objects_name.value,
cpmi.FF_CHILDREN_COUNT % self.objects_name.value,
cpmeas.COLTYPE_INTEGER),
(self.objects_name.value,
cpmi.FF_PARENT % self.new_primary_objects_name.value,
cpmeas.COLTYPE_INTEGER)]
columns += [
(self.primary_objects.value,
cpmi.FF_CHILDREN_COUNT % self.new_primary_objects_name.value,
cpmeas.COLTYPE_INTEGER),
(self.new_primary_objects_name.value,
cpmi.FF_PARENT % self.primary_objects.value,
cpmeas.COLTYPE_INTEGER)
]
return columns
def get_measurement_columns(self, pipeline):
'''Return column definitions for measurements made by this module'''
columns = cpmi.get_object_measurement_columns(self.objects_name.value)
columns += [(self.primary_objects.value,
cpmi.FF_CHILDREN_COUNT%self.objects_name.value,
cpmeas.COLTYPE_INTEGER),
(self.objects_name.value,
cpmi.FF_PARENT%self.primary_objects.value,
cpmeas.COLTYPE_INTEGER)]
if self.method != M_DISTANCE_N:
columns += cpmi.get_threshold_measurement_columns(self.objects_name.value)
if self.wants_discard_edge and self.wants_discard_primary:
columns += cpmi.get_object_measurement_columns(self.new_primary_objects_name.value)
columns += [(self.new_primary_objects_name.value,
cpmi.FF_CHILDREN_COUNT%self.objects_name.value,
cpmeas.COLTYPE_INTEGER),
(self.objects_name.value,
cpmi.FF_PARENT%self.new_primary_objects_name.value,
cpmeas.COLTYPE_INTEGER)]
columns += [(self.primary_objects.value,
cpmi.FF_CHILDREN_COUNT%self.new_primary_objects_name.value,
cpmeas.COLTYPE_INTEGER),
(self.new_primary_objects_name.value,
cpmi.FF_PARENT%self.primary_objects.value,
cpmeas.COLTYPE_INTEGER)]
return columns
def get_measurement_columns(self, pipeline):
'''Return column definitions for measurements made by this module'''
columns = identify.get_object_measurement_columns(self.objects_name.value)
columns += [(self.primary_objects.value,
cellprofiler.measurement.FF_CHILDREN_COUNT % self.objects_name.value,
cellprofiler.measurement.COLTYPE_INTEGER),
(self.objects_name.value,
cellprofiler.measurement.FF_PARENT % self.primary_objects.value,
cellprofiler.measurement.COLTYPE_INTEGER)]
if self.method != M_DISTANCE_N:
columns += super(IdentifySecondaryObjects, self).get_measurement_columns(pipeline)
if self.wants_discard_edge and self.wants_discard_primary:
columns += identify.get_object_measurement_columns(self.new_primary_objects_name.value)
columns += [(self.new_primary_objects_name.value,
cellprofiler.measurement.FF_CHILDREN_COUNT % self.objects_name.value,
cellprofiler.measurement.COLTYPE_INTEGER),
(self.objects_name.value,
cellprofiler.measurement.FF_PARENT % self.new_primary_objects_name.value,
cellprofiler.measurement.COLTYPE_INTEGER)]
columns += [(self.primary_objects.value,
cellprofiler.measurement.FF_CHILDREN_COUNT % self.new_primary_objects_name.value,
cellprofiler.measurement.COLTYPE_INTEGER),
(self.new_primary_objects_name.value,
cellprofiler.measurement.FF_PARENT % self.primary_objects.value,
cellprofiler.measurement.COLTYPE_INTEGER)]
return columns
def get_measurement_columns(self, pipeline):
columns = []
for file_setting in self.file_settings:
if file_setting.image_objects_choice == IO_IMAGES:
image_name = file_setting.image_name.value
path_name_category = C_PATH_NAME
file_name_category = C_FILE_NAME
columns += [
(cpmeas.IMAGE, "_".join((C_MD5_DIGEST, image_name)),
cpmeas.COLTYPE_VARCHAR_FORMAT % 32),
(cpmeas.IMAGE, "_".join(
(C_SCALING, image_name)), cpmeas.COLTYPE_FLOAT),
(cpmeas.IMAGE, "_".join(
(C_HEIGHT, image_name)), cpmeas.COLTYPE_INTEGER),
(cpmeas.IMAGE, "_".join(
(C_WIDTH, image_name)), cpmeas.COLTYPE_INTEGER)
]
else:
image_name = file_setting.objects_name.value
path_name_category = C_OBJECTS_PATH_NAME
file_name_category = C_OBJECTS_FILE_NAME
columns += get_object_measurement_columns(image_name)
columns += [(cpmeas.IMAGE, '_'.join(
(feature, image_name)), coltype) for feature, coltype in (
(file_name_category, cpmeas.COLTYPE_VARCHAR_FILE_NAME),
(path_name_category, cpmeas.COLTYPE_VARCHAR_PATH_NAME),
)]
return columns
def get_measurement_columns(self, pipeline):
columns = []
for file_setting in self.file_settings:
if file_setting.image_objects_choice == IO_IMAGES:
image_name = file_setting.image_name.value
path_name_category = C_PATH_NAME
file_name_category = C_FILE_NAME
columns += [
(cpmeas.IMAGE, "_".join((C_MD5_DIGEST, image_name)), cpmeas.COLTYPE_VARCHAR_FORMAT % 32),
(cpmeas.IMAGE, "_".join((C_SCALING, image_name)), cpmeas.COLTYPE_FLOAT),
(cpmeas.IMAGE, "_".join((C_HEIGHT, image_name)), cpmeas.COLTYPE_INTEGER),
(cpmeas.IMAGE, "_".join((C_WIDTH, image_name)), cpmeas.COLTYPE_INTEGER),
]
else:
image_name = file_setting.objects_name.value
path_name_category = C_OBJECTS_PATH_NAME
file_name_category = C_OBJECTS_FILE_NAME
columns += get_object_measurement_columns(image_name)
columns += [
(cpmeas.IMAGE, "_".join((feature, image_name)), coltype)
for feature, coltype in (
(file_name_category, cpmeas.COLTYPE_VARCHAR_FILE_NAME),
(path_name_category, cpmeas.COLTYPE_VARCHAR_PATH_NAME),
)
]
return columns
def get_measurement_columns(self, pipeline):
'''Return database info on measurements made in module
pipeline - pipeline being run
Return a list of tuples of object name, measurement name and data type
'''
result = I.get_object_measurement_columns(self.objects_name.value)
return result
def get_measurement_columns(self, pipeline):
'''Return database info on measurements made in module
pipeline - pipeline being run
Return a list of tuples of object name, measurement name and data type
'''
result = I.get_object_measurement_columns(self.objects_name.value)
return result
def get_measurement_columns(self, pipeline):
"""Return column definitions for measurements made by this module"""
subregion_name = self.subregion_objects_name.value
columns = cpmi.get_object_measurement_columns(subregion_name)
for parent in (self.primary_objects_name.value, self.secondary_objects_name.value):
columns += [
(parent, cpmi.FF_CHILDREN_COUNT % subregion_name, cpmeas.COLTYPE_INTEGER),
(subregion_name, cpmi.FF_PARENT % parent, cpmeas.COLTYPE_INTEGER),
]
return columns
def get_measurement_columns(self, pipeline):
'''Return column definitions for measurements made by this module'''
object_name = self.object_name.value
remaining_object_name = self.remaining_objects.value
columns = I.get_object_measurement_columns(self.remaining_objects.value)
columns += [(object_name, I.FF_CHILDREN_COUNT % remaining_object_name,
cpmeas.COLTYPE_INTEGER),
(remaining_object_name, I.FF_PARENT % object_name,
cpmeas.COLTYPE_INTEGER)]
return columns
def get_measurement_columns(self, pipeline):
'''Return column definitions for measurements made by this module'''
object_name = self.object_name.value
remaining_object_name = self.remaining_objects.value
columns = I.get_object_measurement_columns(self.remaining_objects.value)
columns += [(object_name, I.FF_CHILDREN_COUNT % remaining_object_name,
cpmeas.COLTYPE_INTEGER),
(remaining_object_name, I.FF_PARENT % object_name,
cpmeas.COLTYPE_INTEGER)]
return columns
def get_measurement_columns(self, pipeline):
'''Return column definitions for measurements made by this module'''
subregion_name = self.subregion_objects_name.value
columns = cpmi.get_object_measurement_columns(subregion_name)
for parent in (self.primary_objects_name.value,
self.secondary_objects_name.value):
columns += [(parent, cpmi.FF_CHILDREN_COUNT % subregion_name,
cpmeas.COLTYPE_INTEGER),
(subregion_name, cpmi.FF_PARENT % parent,
cpmeas.COLTYPE_INTEGER)]
return columns
def get_measurement_columns(self, pipeline):
'''Return information to use when creating database columns'''
orig_image_name = self.object_name.value
filtered_image_name = self.filtered_objects.value
columns = I.get_object_measurement_columns(filtered_image_name)
columns += [(orig_image_name,
I.FF_CHILDREN_COUNT % filtered_image_name,
cpmeas.COLTYPE_INTEGER),
(filtered_image_name,
I.FF_PARENT % orig_image_name,
cpmeas.COLTYPE_INTEGER)]
return columns
def get_measurement_columns(self, pipeline):
'''Return information to use when creating database columns'''
orig_image_name = self.object_name.value
filtered_image_name = self.filtered_objects.value
columns = I.get_object_measurement_columns(filtered_image_name)
columns += [
(orig_image_name, I.FF_CHILDREN_COUNT % filtered_image_name,
cpmeas.COLTYPE_INTEGER),
(filtered_image_name, I.FF_PARENT % orig_image_name,
cpmeas.COLTYPE_INTEGER)
]
return columns
def get_measurement_columns(self, pipeline):
'''Return columns that define the measurements produced by this module'''
result = get_object_measurement_columns(self.straightened_objects_name.value)
if self.wants_measurements:
nsegments = self.number_of_segments.value
nstripes = self.number_of_stripes.value
if nsegments > 1:
result += [(self.straightened_objects_name.value,
"_".join((C_WORM, ftr,
group.straightened_image_name.value,
self.get_scale_name(None, segment))),
cpmeas.COLTYPE_FLOAT)
for ftr, group, segment
in product((FTR_MEAN_INTENSITY, FTR_STD_INTENSITY),
self.images,
range(nsegments))]
if nstripes > 1:
result += [(self.straightened_objects_name.value,
"_".join((C_WORM, ftr,
group.straightened_image_name.value,
self.get_scale_name(stripe, None))),
cpmeas.COLTYPE_FLOAT)
for ftr, group, stripe
in product((FTR_MEAN_INTENSITY, FTR_STD_INTENSITY),
self.images,
range(nstripes))]
if nsegments > 1 and nstripes > 1:
result += [(self.straightened_objects_name.value,
"_".join((C_WORM, ftr,
group.straightened_image_name.value,
self.get_scale_name(stripe, segment))),
cpmeas.COLTYPE_FLOAT)
for ftr, group, stripe, segment
in product((FTR_MEAN_INTENSITY, FTR_STD_INTENSITY),
self.images,
range(nstripes),
range(nsegments))]
return result
def get_measurement_columns(self, pipeline):
'''Return columns that define the measurements produced by this module'''
result = get_object_measurement_columns(self.straightened_objects_name.value)
if self.wants_measurements:
nsegments = self.number_of_segments.value
nstripes = self.number_of_stripes.value
if nsegments > 1:
result += [(self.straightened_objects_name.value,
"_".join((C_WORM, ftr,
group.straightened_image_name.value,
self.get_scale_name(None, segment))),
cpmeas.COLTYPE_FLOAT)
for ftr, group, segment
in product((FTR_MEAN_INTENSITY, FTR_STD_INTENSITY),
self.images,
range(nsegments))]
if nstripes > 1:
result += [(self.straightened_objects_name.value,
"_".join((C_WORM, ftr,
group.straightened_image_name.value,
self.get_scale_name(stripe, None))),
cpmeas.COLTYPE_FLOAT)
for ftr, group, stripe
in product((FTR_MEAN_INTENSITY, FTR_STD_INTENSITY),
self.images,
range(nstripes))]
if nsegments > 1 and nstripes > 1:
result += [(self.straightened_objects_name.value,
"_".join((C_WORM, ftr,
group.straightened_image_name.value,
self.get_scale_name(stripe, segment))),
cpmeas.COLTYPE_FLOAT)
for ftr, group, stripe, segment
in product((FTR_MEAN_INTENSITY, FTR_STD_INTENSITY),
self.images,
range(nstripes),
range(nsegments))]
return result