def _read_component_image(self, filename):
stack = read_tiff_stack(filename)
channels = []
for raw in stack:
meta = raw['raw_meta']
image_type, image_description = self._parse_image_description(
meta['ImageDescription'])
#image_type, image_description = self._parse_image_description(meta['ImageDescription'])
if 'ImageType' not in image_description: continue
if image_description['ImageType'] == 'ReducedResolution': continue
if 'Name' not in image_description: continue
channel_label = image_description['Name']
image_id = uuid4().hex
if self._storage_type is not None:
self._images[image_id] = raw['raw_image'].astype(
self._storage_type)
else:
self._images[image_id] = raw['raw_image']
channels.append((channel_label, image_id))
df = pd.DataFrame(channels, columns=['channel_label', 'image_id'])
temp = self.get_data('measurement_channels').drop(
columns=['image_id']).reset_index().merge(df,
on='channel_label',
how='left')
self.set_data('measurement_channels', temp.set_index('channel_index'))
return
def _read_seg_images(self, memb_seg_image_file, nuc_seg_image_file):
segmentation_names = []
memb = make_binary_image_array(
read_tiff_stack(memb_seg_image_file)[0]['raw_image'])
memb_id = uuid4().hex
self._images[memb_id] = memb.astype(int)
segmentation_names.append(['Membrane', memb_id])
nuc = read_tiff_stack(nuc_seg_image_file)[0]['raw_image']
nuc_id = uuid4().hex
self._images[nuc_id] = nuc.astype(int)
segmentation_names.append(['Nucleus', nuc_id])
#_mask_key = pd.DataFrame(mask_names,columns=['mask_label','image_id'])
#_mask_key.index.name = 'db_id'
#self.set_data('mask_images',_mask_key)
_segmentation_key = pd.DataFrame(
segmentation_names, columns=['segmentation_label', 'image_id'])
_segmentation_key.index.name = 'db_id'
self.set_data('segmentation_images', _segmentation_key)
def set_line_area(self, line_image, area_image, steps=20, verbose=False):
drawn_binary = np.zeros(self.shape)
if os.path.exists(line_image):
drawn_binary = read_tiff_stack(line_image)[0]['raw_image']
drawn_binary = make_binary_image_array(drawn_binary)
elif verbose:
sys.stderr.write(
"Skipping the invasive margin since there is none present.\n")
image_id1 = uuid4().hex
self._images[image_id1] = drawn_binary
area_binary = read_tiff_stack(area_image)[0]['raw_image']
area_binary = make_binary_image_array(area_binary)
image_id2 = uuid4().hex
self._images[image_id2] = area_binary
df = pd.DataFrame({
'custom_label': ['Drawn', 'Area'],
'image_id': [image_id1, image_id2]
})
df.index.name = 'db_id'
self.set_data('custom_images', df)
grown = binary_image_dilation(drawn_binary, steps=steps)
processed_image = self.get_image(self.processed_image_id).astype(
np.uint8)
margin_binary = grown & processed_image
tumor_binary = (area_binary & (~grown)) & processed_image
stroma_binary = (~(
(tumor_binary | grown) & processed_image)) & processed_image
d = {
'Margin': margin_binary,
'Tumor': tumor_binary,
'Stroma': stroma_binary
}
self.set_regions(d)
return d
def _read_component_image(self, filename):
stack = read_tiff_stack(filename)
channels = []
for i, raw in enumerate(stack):
meta = raw['raw_meta']['image_description']
markers = [x.split('=')[1] for x in meta.split('\n')[1:]]
channel_label = markers[i]
image_id = uuid4().hex
self._images[image_id] = raw['raw_image'].astype(
self._storage_type)
channels.append((channel_label, image_id))
df = pd.DataFrame(channels, columns=['channel_label', 'image_id'])
temp = self.get_data('measurement_channels').drop(
columns=['image_id']).reset_index().merge(df,
on='channel_label',
how='left')
self.set_data('measurement_channels', temp.set_index('channel_index'))
return
def _read_component_image(self, filename, channel_abbreviations):
stack = read_tiff_stack(filename)
channels = []
for index, v in enumerate(stack):
img = v['raw_image']
meta = v['raw_meta']
image_description = json.loads(meta['ImageDescription'])
channel_label = image_description['channel.target']
image_id = uuid4().hex
channels.append((channel_label, image_id))
self._images[image_id] = img # saving image
df = pd.DataFrame(channels, columns=['channel_label', 'image_id'])
df['channel_abbreviation'] = df['channel_label'].apply(
lambda x: x
if x not in channel_abbreviations else channel_abbreviations[x])
df.index.name = 'channel_index'
self.set_data('measurement_channels', df)
return
def set_area(self,
area_image,
custom_mask_name,
other_mask_name,
verbose=False):
area_binary = read_tiff_stack(area_image)[0]['raw_image']
area_binary = make_binary_image_array(area_binary)
image_id = uuid4().hex
self._images[image_id] = area_binary
df = pd.DataFrame({'custom_label': ['Area'], 'image_id': [image_id]})
df.index.name = 'db_id'
self.set_data('custom_images', df)
processed_image = self.get_image(self.processed_image_id).astype(
np.uint8)
#margin_binary = grown&processed_image
tumor_binary = area_binary & processed_image
stroma_binary = (~(tumor_binary & processed_image)) & processed_image
d = {custom_mask_name: tumor_binary, other_mask_name: stroma_binary}
self.set_regions(d)
return d
def _read_binary_seg_image(self, filename):
stack = read_tiff_stack(filename)
mask_names = []
segmentation_names = []
for raw in stack:
meta = raw['raw_meta']
image_type, image_description = self._parse_image_description(
meta['ImageDescription'])
#print("parsing image description")
#print("meta: "+str(meta))
#print("image_type: "+str(image_type))
#print("image_description: "+str(image_description))
image_id = uuid4().hex
if image_type == 'SegmentationImage':
### Handle if its a segmentation
self._images[image_id] = raw['raw_image'].astype(int)
segmentation_names.append(
[image_description['CompartmentType'], image_id])
else:
### Otherwise it is a mask
self._images[image_id] = raw['raw_image'].astype(int)
mask_names.append([image_type, image_id])
### If we have a Tissue Class Map we should process it into regions
if image_type == 'TissueClassMap':
# Process the Tissue Class Map
self._process_tissue_class_map(
image_description, raw['raw_image'].astype(int))
_mask_key = pd.DataFrame(mask_names,
columns=['mask_label', 'image_id'])
_mask_key.index.name = 'db_id'
self.set_data('mask_images', _mask_key)
_segmentation_key = pd.DataFrame(
segmentation_names, columns=['segmentation_label', 'image_id'])
_segmentation_key.index.name = 'db_id'
self.set_data('segmentation_images', _segmentation_key)
def _read_data(self, annotations, mibi_cell_labels_tif_path):
""" Read in the image data from MIBI using mibitracker
:param cell_seg_data_file:
:type string:
"""
cell_labels = read_tiff_stack(
mibi_cell_labels_tif_path)[0]['raw_image']
if self.verbose:
sys.stderr.write(
"Calling mibitracker cell total intensity scores\n")
#_seg = mibi_segmentation.extract_cell_dataframe(cell_labels, mibi_tiff.read(mibi_component_tif_path), mode='total')
#print(_seg)
#if 'Tissue Category' not in _seg: _seg['Tissue Category'] = 'Any'
_cells = pd.DataFrame(annotations).set_index('cell_index')
###########
# Set dummy values for the cell phenotypes
_phenotypes = _cells.copy().drop(columns=['x', 'y'])
#_phenotypes['phenotype_label'] = np.nan
_phenotypes = _phenotypes.loc[:, ['phenotype_label']]
_phenotypes_present = pd.Series(
_phenotypes['phenotype_label'].unique()).tolist()
_phenotypes_present = [np.nan]
_phenotype_list = pd.DataFrame(
{'phenotype_label': _cells['phenotype_label'].unique()})
_phenotype_list.index.name = 'phenotype_index'
_phenotype_list = _phenotype_list.reset_index()
_phenotypes = _phenotypes.reset_index().merge(
_phenotype_list, on='phenotype_label').set_index('cell_index')
_phenotype_list = _phenotype_list.set_index('phenotype_index')
#Assign 'phenotypes' in a way that ensure we retain the pre-defined column structure
self.set_data('phenotypes', _phenotype_list)
if self.verbose:
sys.stderr.write("Finished assigning phenotype list.\n")
_phenotypes = _phenotypes.drop(
columns=['phenotype_label']).applymap(int)
# Now we can add to cells our phenotype indecies
_cells = _cells.merge(_phenotypes,
left_index=True,
right_index=True,
how='left')
###########
# Set the cell_regions
_cell_regions = _cells[['x']].copy()
_cell_regions['region_label'] = 'Any'
_cell_regions = _cell_regions.drop(columns=['x'])
_cell_regions = _cell_regions.reset_index().merge(
self.get_data('regions')[['region_label']].reset_index(),
on='region_label')
_cell_regions = _cell_regions.drop(
columns=['region_label']).set_index('cell_index')
# Now we can add to cells our region indecies
_cells = _cells.merge(_cell_regions,
left_index=True,
right_index=True,
how='left').drop(columns=['phenotype_label'])
# Assign 'cells' in a way that ensures we retain our pre-defined column structure. Should throw a warning if anything is wrong
self.set_data('cells', _cells)
if self.verbose:
sys.stderr.write(
"Finished setting the cell list regions are set.\n")
###########
# Get the intensity measurements - sets 'measurement_channels', 'measurement_statistics', 'measurement_features', and 'cell_measurements'
#'cell_measurements':{'index':'measurement_index',
# 'columns':['cell_index','statistic_index','feature_index','channel_index','value']},
#'measurement_features':{'index':'feature_index',
# 'columns':['feature_label']},
#'measurement_statistics':{'index':'statistic_index',
# 'columns':['statistic_label']},
#_seg2 = _seg.reset_index().set_index(['label','area','x_centroid','y_centroid']).\
# stack().reset_index().rename(columns={'level_4':'marker',0:'Total'})
#_seg2['feature_label'] = 'Total'
#if self.verbose: sys.stderr.write("Calling mibitracker circular_sectors with 4 sectors\n")
#_seg3 = mibi_segmentation.extract_cell_dataframe(cell_labels, mibi_tiff.read(mibi_component_tif_path), mode='circular_sectors', num_sectors=4).\
# reset_index().set_index(['label','area','x_centroid','y_centroid']).\
# stack().reset_index().rename(columns={'level_4':'marker',0:'Total'})
#_seg3['feature_label'] = 'Circular Sectors 4'
#if self.verbose: sys.stderr.write("Calling mibitracker circular_sectors with 8 sectors\n")
#_seg4 = mibi_segmentation.extract_cell_dataframe(cell_labels, mibi_tiff.read(mibi_component_tif_path), mode='circular_sectors', num_sectors=8).\
# reset_index().set_index(['label','area','x_centroid','y_centroid']).\
# stack().reset_index().rename(columns={'level_4':'marker',0:'Total'})
#_seg4['feature_label'] = 'Circular Sectors 8'
#_segs = pd.concat([_seg2,_seg3,_seg4])
#_segs['Mean'] = _segs.apply(lambda x: x['Total']/x['area'],1)
#_segs = _segs.rename(columns={'label':'cell_index','marker':'channel_label'}).\
# drop(columns=['area','x_centroid','y_centroid']).set_index(['cell_index','channel_label','feature_label']).\
# stack().reset_index().rename(columns={0:'value','level_3':'statistic_label'})
_measurement_statistics = pd.DataFrame([[0,'Total']],columns=['statistic_index','statistic_label']).\
set_index('statistic_index')
self.set_data('measurement_statistics', _measurement_statistics)
_measurement_features = pd.DataFrame({'feature_label': ['Total']})
_measurement_features.index.name = 'feature_index'
self.set_data('measurement_features', _measurement_features)
_cell_measurements = pd.DataFrame(
(),
columns=[
'cell_index', 'statistic_index', 'feature_index',
'channel_index', 'value'
])
_cell_measurements.index.name = 'measurement_index'
self.set_data('cell_measurements', _cell_measurements)
if self.verbose:
sys.stderr.write("Finished setting the measurements.\n")
###########
return
def _read_seg_image(self, mibi_cell_labels_tif_path,
generate_processed_area_image,
processed_area_image_steps):
# Do our segmentation first
cell_labels = read_tiff_stack(
mibi_cell_labels_tif_path)[0]['raw_image']
image_id = uuid4().hex
self._images[image_id] = cell_labels
segmentation_names = [['Membrane', image_id]]
_segmentation_key = pd.DataFrame(
segmentation_names, columns=['segmentation_label', 'image_id'])
_segmentation_key.index.name = 'db_id'
self.set_data('segmentation_images', _segmentation_key)
# make the cell map to be a copy of the membrane segmentation
cell_map_id = uuid4().hex
self._images[cell_map_id] = cell_labels.copy()
increment = self.get_data('segmentation_images').index.max() + 1
extra = pd.DataFrame(
pd.Series(
dict({
'db_id': increment,
'segmentation_label': 'cell_map',
'image_id': cell_map_id
}))).T
extra = pd.concat(
[self.get_data('segmentation_images'),
extra.set_index('db_id')])
self.set_data('segmentation_images', extra)
# make the edge map incrementally
edge_map_id = uuid4().hex
self._images[edge_map_id] = image_edges(cell_labels)
increment = self.get_data('segmentation_images').index.max() + 1
extra = pd.DataFrame(
pd.Series(
dict({
'db_id': increment,
'segmentation_label': 'edge_map',
'image_id': edge_map_id
}))).T
extra = pd.concat(
[self.get_data('segmentation_images'),
extra.set_index('db_id')])
self.set_data('segmentation_images', extra)
image_id = uuid4().hex
mask_names = [['ProcessRegionImage', image_id]]
processed = make_binary_image_array(np.ones(cell_labels.shape))
self._images[image_id] = processed
if self.verbose:
sys.stderr.write("size of image: " + str(processed.sum().sum()) +
"\n")
if generate_processed_area_image:
if self.verbose:
sys.stderr.write(
"Creating approximate processed_image_area by watershed.\n"
)
processed = binary_image_dilation(
make_binary_image_array(cell_labels),
steps=processed_area_image_steps)
self._images[image_id] = processed
_mask_key = pd.DataFrame(mask_names,
columns=['mask_label', 'image_id'])
_mask_key.index.name = 'db_id'
self.set_data('mask_images', _mask_key)
self.set_processed_image_id(image_id)
self._images[self.processed_image_id] = processed.astype(np.int8)
if self.verbose:
sys.stderr.write("size of processed image: " +
str(processed.sum().sum()) + "\n")
