def get_measurement_columns(self, pipeline):
'''Return a sequence describing the measurement columns needed by this module
'''
cols = []
for fd in self.images:
name = fd[FD_IMAGE_NAME].value
cols += [('Image', 'FileName_' + name,
cpm.COLTYPE_VARCHAR_FILE_NAME)]
cols += [('Image', 'PathName_' + name,
cpm.COLTYPE_VARCHAR_PATH_NAME)]
cols += [('Image', 'MD5Digest_' + name,
cpm.COLTYPE_VARCHAR_FORMAT % 32)]
fd = self.images[0]
if fd[FD_METADATA_CHOICE] == M_FILE_NAME or fd[
FD_METADATA_CHOICE] == M_BOTH:
tokens = cpm.find_metadata_tokens(fd[FD_FILE_METADATA].value)
cols += [('Image', 'Metadata_' + token,
cpm.COLTYPE_VARCHAR_FILE_NAME) for token in tokens]
if fd[FD_METADATA_CHOICE] == M_PATH or fd[FD_METADATA_CHOICE] == M_BOTH:
tokens = cpm.find_metadata_tokens(fd[FD_PATH_METADATA].value)
cols += [('Image', 'Metadata_' + token,
cpm.COLTYPE_VARCHAR_PATH_NAME) for token in tokens]
return cols
def run_objects(self, object_names, file_name, workspace):
"""Create a file (or files if there's metadata) based on the object names
object_names - a sequence of object names (or Image or Experiment)
which tell us which objects get piled into each file
file_name - a file name or file name with metadata tags to serve as the
output file.
workspace - get the images from here.
"""
if len(object_names) == 1 and object_names[0] == EXPERIMENT:
self.make_experiment_file(file_name, workspace)
return
tags = cpmeas.find_metadata_tokens(file_name)
if self.directory.is_custom_choice:
tags += cpmeas.find_metadata_tokens(self.directory.custom_path)
metadata_groups = workspace.measurements.group_by_metadata(tags)
for metadata_group in metadata_groups:
if len(object_names) == 1 and object_names[0] == IMAGE:
self.make_image_file(file_name,
metadata_group.image_numbers,
workspace)
if self.wants_genepattern_file.value:
self.make_gct_file(file_name,
metadata_group.image_numbers,
workspace)
elif len(object_names) == 1 and object_names[0] == OBJECT_RELATIONSHIPS:
self.make_relationships_file(file_name,
metadata_group.image_numbers,
workspace)
else:
self.make_object_file(object_names, file_name,
metadata_group.image_numbers, workspace)
def run_objects(self, object_names, file_name, workspace):
"""Create a file (or files if there's metadata) based on the object names
object_names - a sequence of object names (or Image or Experiment)
which tell us which objects get piled into each file
file_name - a file name or file name with metadata tags to serve as the
output file.
workspace - get the images from here.
"""
if len(object_names) == 1 and object_names[0] == EXPERIMENT:
self.make_experiment_file(file_name, workspace)
return
tags = cpmeas.find_metadata_tokens(file_name)
if self.directory.is_custom_choice:
tags += cpmeas.find_metadata_tokens(self.directory.custom_path)
metadata_groups = workspace.measurements.group_by_metadata(tags)
for metadata_group in metadata_groups:
if len(object_names) == 1 and object_names[0] == IMAGE:
self.make_image_file(file_name, metadata_group.image_numbers,
workspace)
if self.wants_genepattern_file.value:
self.make_gct_file(file_name, metadata_group.image_numbers,
workspace)
elif len(object_names
) == 1 and object_names[0] == OBJECT_RELATIONSHIPS:
self.make_relationships_file(file_name,
metadata_group.image_numbers,
workspace)
else:
self.make_object_file(object_names, file_name,
metadata_group.image_numbers, workspace)
def get_metadata_groups(self, workspace, settings_group=None):
'''Find the metadata groups that are relevant for creating the file name
workspace - the workspace with the image set metadata elements and
grouping measurements populated.
settings_group - if saving individual objects, this is the settings
group that controls naming the files.
'''
if settings_group is None or settings_group.wants_automatic_file_name:
tags = []
else:
tags = cpmeas.find_metadata_tokens(settings_group.file_name.value)
if self.directory.is_custom_choice:
tags += cpmeas.find_metadata_tokens(self.directory.custom_path)
metadata_groups = workspace.measurements.group_by_metadata(tags)
return metadata_groups
def get_metadata_tags(self, fd=None):
"""Find the metadata tags for the indexed image
fd - an image file directory from self.images
"""
if not fd:
s = set()
for fd in self.images:
s.update(self.get_metadata_tags(fd))
tags = list(s)
tags.sort()
return tags
tags = []
if fd[FD_METADATA_CHOICE] in (M_FILE_NAME, M_BOTH):
tags += cpm.find_metadata_tokens(fd[FD_FILE_METADATA].value)
if fd[FD_METADATA_CHOICE] in (M_PATH, M_BOTH):
tags += cpm.find_metadata_tokens(fd[FD_PATH_METADATA].value)
return tags
def get_metadata_tags(self, fd=None):
"""Find the metadata tags for the indexed image
fd - an image file directory from self.images
"""
if not fd:
s = set()
for fd in self.images:
s.update(self.get_metadata_tags(fd))
tags = list(s)
tags.sort()
return tags
tags = []
if fd[FD_METADATA_CHOICE] in (M_FILE_NAME, M_BOTH):
tags += cpm.find_metadata_tokens(fd[FD_FILE_METADATA].value)
if fd[FD_METADATA_CHOICE] in (M_PATH, M_BOTH):
tags += cpm.find_metadata_tokens(fd[FD_PATH_METADATA].value)
return tags
def get_measurement_columns(self, pipeline):
'''Return a sequence describing the measurement columns needed by this module
'''
cols = []
for fd in self.images:
name = fd[FD_IMAGE_NAME].value
cols += [('Image','FileName_'+name, cpm.COLTYPE_VARCHAR_FILE_NAME)]
cols += [('Image','PathName_'+name, cpm.COLTYPE_VARCHAR_PATH_NAME)]
cols += [('Image','MD5Digest_'+name, cpm.COLTYPE_VARCHAR_FORMAT%32)]
fd = self.images[0]
if fd[FD_METADATA_CHOICE]==M_FILE_NAME or fd[FD_METADATA_CHOICE]==M_BOTH:
tokens = cpm.find_metadata_tokens(fd[FD_FILE_METADATA].value)
cols += [('Image', 'Metadata_'+token, cpm.COLTYPE_VARCHAR_FILE_NAME) for token in tokens]
if fd[FD_METADATA_CHOICE]==M_PATH or fd[FD_METADATA_CHOICE]==M_BOTH:
tokens = cpm.find_metadata_tokens(fd[FD_PATH_METADATA].value)
cols += [('Image', 'Metadata_'+token, cpm.COLTYPE_VARCHAR_PATH_NAME) for token in tokens]
return cols
def update_imported_metadata(self):
new_imported_metadata = []
ipd_metadata_keys = set(getattr(self, "ipd_metadata_keys", []))
for group in self.extraction_methods:
if group.extraction_method == X_MANUAL_EXTRACTION:
if group.source == XM_FILE_NAME:
regexp = group.file_regexp
else:
regexp = group.folder_regexp
ipd_metadata_keys.update(
cpmeas.find_metadata_tokens(regexp.value))
elif group.extraction_method == X_IMPORTED_EXTRACTION:
joiner = group.csv_joiner
csv_path = group.csv_location.value
if not os.path.isfile(csv_path):
continue
found = False
best_match = None
for i, imported_metadata in enumerate(self.imported_metadata):
assert isinstance(imported_metadata, self.ImportedMetadata)
if imported_metadata.is_match(csv_path, joiner,
self.CSV_JOIN_NAME,
self.IPD_JOIN_NAME):
new_imported_metadata.append(imported_metadata)
found = True
break
elif (best_match is None
and imported_metadata.path == csv_path):
best_match = i
if found:
del self.imported_metadata[i]
else:
if best_match is not None:
imported_metadata = self.imported_metadata[i]
del self.imported_metadata[i]
else:
try:
imported_metadata = self.ImportedMetadata(csv_path)
except:
logger.debug("Failed to load csv file: %s" %
csv_path)
continue
new_imported_metadata.append(imported_metadata)
joiner.entities[self.CSV_JOIN_NAME] = \
imported_metadata.get_csv_metadata_keys()
joiner.entities[self.IPD_JOIN_NAME] = \
list(ipd_metadata_keys)
imported_metadata.set_joiner(joiner, self.CSV_JOIN_NAME,
self.IPD_JOIN_NAME)
ipd_metadata_keys.update(
imported_metadata.get_csv_metadata_keys())
self.imported_metadata = new_imported_metadata
def update_imported_metadata(self):
new_imported_metadata = []
ipd_metadata_keys = set(getattr(self, "ipd_metadata_keys", []))
for group in self.extraction_methods:
if group.extraction_method == X_MANUAL_EXTRACTION:
if group.source == XM_FILE_NAME:
regexp = group.file_regexp
else:
regexp = group.folder_regexp
ipd_metadata_keys.update(cpmeas.find_metadata_tokens(regexp.value))
elif group.extraction_method == X_IMPORTED_EXTRACTION:
joiner = group.csv_joiner
csv_path = group.csv_location.value
if not os.path.isfile(csv_path):
continue
found = False
best_match = None
for i, imported_metadata in enumerate(self.imported_metadata):
assert isinstance(imported_metadata, self.ImportedMetadata)
if imported_metadata.is_match(csv_path, joiner,
self.CSV_JOIN_NAME,
self.IPD_JOIN_NAME):
new_imported_metadata.append(imported_metadata)
found = True
break
elif (best_match is None and
imported_metadata.path == csv_path):
best_match = i
if found:
del self.imported_metadata[i]
else:
if best_match is not None:
imported_metadata = self.imported_metadata[i]
del self.imported_metadata[i]
else:
try:
imported_metadata = self.ImportedMetadata(csv_path)
except:
logger.debug("Failed to load csv file: %s" % csv_path)
continue
new_imported_metadata.append(imported_metadata)
joiner.entities[self.CSV_JOIN_NAME] = \
imported_metadata.get_csv_metadata_keys()
joiner.entities[self.IPD_JOIN_NAME] = \
list(ipd_metadata_keys)
imported_metadata.set_joiner(joiner,
self.CSV_JOIN_NAME,
self.IPD_JOIN_NAME)
ipd_metadata_keys.update(imported_metadata.get_csv_metadata_keys())
self.imported_metadata = new_imported_metadata
def validate_module(self, pipeline):
'''Validate the module settings
pipeline - current pipeline
Metadata throws an exception if any of the metadata tags collide with
tags that can be automatically extracted.
'''
for group in self.extraction_methods:
if group.extraction_method == X_MANUAL_EXTRACTION:
re_setting = (group.file_regexp if group.source == XM_FILE_NAME
else group.folder_regexp)
for token in cpmeas.find_metadata_tokens(re_setting.value):
if token in cpmeas.RESERVED_METADATA_TAGS:
raise cps.ValidationError(
'The metadata tag, "%s", is reserved for use by CellProfiler. Please use some other tag name.' %
token, re_setting)
def validate_module(self, pipeline):
'''Validate the module settings
pipeline - current pipeline
Metadata throws an exception if any of the metadata tags collide with
tags that can be automatically extracted.
'''
for group in self.extraction_methods:
if group.extraction_method == X_MANUAL_EXTRACTION:
re_setting = (group.file_regexp if group.source == XM_FILE_NAME
else group.folder_regexp)
for token in cpmeas.find_metadata_tokens(re_setting.value):
if token in cpmeas.RESERVED_METADATA_TAGS:
raise cps.ValidationError(
'The metadata tag, "%s", is reserved for use by CellProfiler. Please use some other tag name.'
% token, re_setting)
def get_metadata_keys(self):
"""Return a collection of metadata keys to be associated with files"""
keys = set()
self.update_imported_metadata()
for group in self.extraction_methods:
if group.extraction_method == X_MANUAL_EXTRACTION:
if group.source == XM_FILE_NAME:
regexp = group.file_regexp
else:
regexp = group.folder_regexp
keys.update(cpmeas.find_metadata_tokens(regexp.value))
elif group.extraction_method == X_IMPORTED_EXTRACTION:
imported_metadata = self.get_imported_metadata_for_group(group)
if imported_metadata is None:
logger.warn("Unable to import metadata from %s" % group.csv_location.value)
keys.update(imported_metadata.metadata_keys)
elif group.extraction_method == X_AUTOMATIC_EXTRACTION:
# Assume that automatic extraction will populate T and Z
keys.add(cpp.ImagePlaneDetails.MD_T)
keys.add(cpp.ImagePlaneDetails.MD_Z)
return list(keys)
def get_metadata_keys(self):
'''Return a collection of metadata keys to be associated with files'''
keys = set()
self.update_imported_metadata()
for group in self.extraction_methods:
if group.extraction_method == X_MANUAL_EXTRACTION:
if group.source == XM_FILE_NAME:
regexp = group.file_regexp
else:
regexp = group.folder_regexp
keys.update(cpmeas.find_metadata_tokens(regexp.value))
elif group.extraction_method == X_IMPORTED_EXTRACTION:
imported_metadata = self.get_imported_metadata_for_group(group)
if imported_metadata is None:
logger.warn("Unable to import metadata from %s" %
group.csv_location.value)
keys.update(imported_metadata.metadata_keys)
elif group.extraction_method == X_AUTOMATIC_EXTRACTION:
# Assume that automatic extraction will populate T and Z
keys.add(cpp.ImagePlaneDetails.MD_T)
keys.add(cpp.ImagePlaneDetails.MD_Z)
return list(keys)