def scan_next_frame(self, frame_img, is_single_image=False):
self._frame_img = frame_img
self._frame_number += 1
self._is_single_image = is_single_image
result = OpenScanResult(self._frame_number)
result.set_old_barcode_data(self._old_barcode_data)
result.start_timer()
# Read all the barcodes in the image
try:
barcodes = self._perform_frame_scan()
result.set_barcodes(barcodes)
except NoBarcodesError as ex:
result.set_error(str(ex))
# Create a 'blank' geometry object to store the barcode locations
new_barcodes = result.new_barcodes()
num_barcodes = len(new_barcodes)
geometry = self._create_geometry(new_barcodes)
# Create the plate
if any(new_barcodes):
plate = Plate(self.plate_type, num_slots=num_barcodes)
plate.set_geometry(geometry)
for s, barcode in enumerate(new_barcodes):
plate.slot(s).set_barcode(barcode)
result.set_plate(plate)
result.end_timer()
return result
def _initialize_plate_from_barcodes(self):
for bc in self._barcodes:
bc.perform_read()
if self._any_valid_barcodes():
slot_scanner = self._create_slot_scanner()
self._plate = Plate(self.plate_type)
self._plate_scan = PlateScanner(self._plate, self._is_single_image)
self._plate_scan.new_frame(self._geometry, self._barcodes, slot_scanner)
def _initialize_plate_from_barcodes(self):
for bc in self._barcodes:
bc.perform_read()
if self._any_valid_barcodes():
slot_scanner = self._create_slot_scanner()
self._plate = Plate(self.plate_type)
self._plate_scan = PlateScanner(self._plate, self._is_single_image)
self._plate_scan.new_frame(self._geometry, self._barcodes, slot_scanner)
def scan_next_frame(self, frame_img, is_single_image=False):
self._frame_img = frame_img
self._frame_number += 1
self._is_single_image = is_single_image
result = OpenScanResult(self._frame_number)
result.set_old_barcode_data(self._old_barcode_data)
result.start_timer()
# Read all the barcodes in the image
try:
barcodes = self._perform_frame_scan()
result.set_barcodes(barcodes)
except NoBarcodesDetectedError as ex:
# TODO: logging the error
result.set_error(str(ex))
# Create a 'blank' geometry object to store the barcode locations
new_barcodes = result.new_barcodes()
num_new_barcodes = len(new_barcodes)
geometry = self._create_geometry(new_barcodes)
# Create the plate
if any(new_barcodes):
plate = Plate(self.plate_type, num_slots=num_new_barcodes)
plate.set_geometry(geometry)
for s, barcode in enumerate(new_barcodes):
plate.slot(s).set_barcode(barcode)
result.set_plate(plate)
result.end_timer()
return result
class GeometryScanner:
def __init__(self, plate_type, barcode_sizes):
self.plate_type = plate_type
self.barcode_sizes = barcode_sizes
self._frame_number = 0
self._plate = None
self._plate_scan = None
self._frame_img = None
self._geometry = None
self._barcodes = []
self._is_single_image = False
self._frame_result = None
def scan_next_frame(self, frame_img, is_single_image=False):
self._new_frame()
self._frame_img = frame_img
self._is_single_image = is_single_image
try:
self._perform_frame_scan()
self._frame_result.set_plate(self._plate)
#TODO: use logs
except (NoBarcodesDetectedError, GeometryException,
GeometryAdjustmentError) as ex:
self._frame_result.set_error(str(ex))
self._frame_result.end_timer()
return self._frame_result
def _new_frame(self):
self._frame_img = None
self._geometry = None
self._barcodes = []
self._is_single_image = False
self._frame_number += 1
self._frame_result = ScanResult(self._frame_number)
self._frame_result.set_previous_plate(self._plate)
self._frame_result.start_timer()
def _perform_frame_scan(self):
self._barcodes = self._locate_all_barcodes_in_image()
self._frame_result.set_barcodes(self._barcodes)
if self.plate_type == Geometry.UNIPUCK:
self._geometry = UnipuckLocator(self._frame_img).find_location()
if self._geometry is None:
self._geometry = self._calculate_geometry()
self._frame_result.set_geometry(self._geometry)
# Determine if the previous plate scan has any barcodes in common with this one.
has_common_barcodes, is_same_align = self._find_common_barcode(
self._geometry, self._barcodes)
if has_common_barcodes and self._plate.is_full_valid():
return
elif not has_common_barcodes:
self._initialize_plate_from_barcodes()
elif has_common_barcodes and not is_same_align:
self._geometry = self._adjust_geometry(self._barcodes)
# Merge with old plate
if has_common_barcodes:
self._merge_frame_into_plate()
def _locate_all_barcodes_in_image(self):
barcodes = DataMatrix.locate_all_barcodes_in_image(
self._frame_img, self.barcode_sizes)
# TODO: log this
if len(barcodes) == 0:
raise NoBarcodesDetectedError()
return barcodes
def _calculate_geometry(self):
slot_centers = [bc.center() for bc in self._barcodes]
if self.plate_type == Geometry.UNIPUCK:
use_emptys = len(self._barcodes) < 8
if use_emptys:
empty_circles = EmptySlotDetector.detect(
self._frame_img, self._barcodes)
empty_centers = [c.center() for c in empty_circles]
slot_centers.extend(empty_centers)
geometry = Geometry.calculate_geometry(self.plate_type, slot_centers)
return geometry
def _initialize_plate_from_barcodes(self):
for bc in self._barcodes:
bc.perform_read()
if self._any_valid_barcodes():
slot_scanner = self._create_slot_scanner()
self._plate = Plate(self.plate_type)
self._plate_scan = PlateScanner(self._plate, self._is_single_image)
self._plate_scan.new_frame(self._geometry, self._barcodes,
slot_scanner)
def _merge_frame_into_plate(self):
# If one of the barcodes matches the previous frame and is aligned in the same slot, then we can
# be fairly sure we are dealing with the same plate. Copy all of the barcodes that we read in the
# previous plate over to their slot in the new plate. Then read any that we haven't already read.
slot_scanner = self._create_slot_scanner()
self._plate_scan.new_frame(self._geometry, self._barcodes,
slot_scanner)
def _any_valid_barcodes(self):
return any([bc.is_read() and bc.is_valid() for bc in self._barcodes])
def _create_slot_scanner(self):
slot_scanner = SlotScanner(self._frame_img, self._barcodes)
return slot_scanner
def _find_common_barcode(self, geometry, barcodes):
""" Determine if the set of finder patterns has any barcodes in common with the existing plate.
Return a boolean and a list of the barcodes that have been read. """
has_common_barcodes = False
has_common_geometry = False
num_common_barcodes = 0
# If no plate, don't bother to look for common barcodes
if self._plate is None:
return has_common_barcodes, has_common_geometry
slotted_barcodes = self._make_slotted_barcodes_list(barcodes, geometry)
# Determine if the previous plate scan has any barcodes in common with this one.
for i in range(self._plate.num_slots):
old_slot = self._plate.slot(i)
new_bc = slotted_barcodes[i - 1]
# Only interested in reading barcodes that might match existing ones
if new_bc is None or old_slot.state() != Slot.VALID:
continue
# Read the barcode
new_bc.perform_read()
if not new_bc.is_valid():
continue
num_common_barcodes += 1
has_common_geometry = new_bc.data() == old_slot.barcode_data()
has_common_barcodes = has_common_geometry or self._plate.contains_barcode(
new_bc.data())
# If the geometry of this and the previous frame line up, then we are done. Otherwise we
# need to read at least 2 barcodes so we can perform a realignment.
if has_common_geometry or num_common_barcodes >= 2:
break
return has_common_barcodes, has_common_geometry
@staticmethod
def _make_slotted_barcodes_list(barcodes, geometry):
# Make a list of the unread barcodes with associated slot numbers - from this frame's geometry
slotted_bcs = [None] * geometry.num_slots()
for bc in barcodes:
slot_num = geometry.containing_slot(bc.center())
if slot_num is not None:
slotted_bcs[slot_num - 1] = bc
return slotted_bcs
def _adjust_geometry(self, barcodes):
# If we have a barcode that matches with the previous frame but that isn't in the same slot, then
# at least one of the frames wasn't properly aligned - so we adjust the geometry to match the
# frames together
adjuster = UnipuckGeometryAdjuster()
geometry = adjuster.adjust(self._plate, barcodes)
return geometry
class GeometryScanner:
def __init__(self, plate_type, barcode_size):
self.plate_type = plate_type
self.barcode_size = barcode_size
self._frame_number = 0
self._plate = None
self._plate_scan = None
self._frame_img = None
self._geometry = None
self._barcodes = []
self._is_single_image = False
self._frame_result = None
def scan_next_frame(self, frame_img, is_single_image=False):
self._new_frame()
self._frame_img = frame_img
self._is_single_image = is_single_image
try:
self._perform_frame_scan()
self._frame_result.set_plate(self._plate)
except (NoBarcodesError, GeometryException, GeometryAdjustmentError) as ex:
self._frame_result.set_error(str(ex))
self._frame_result.end_timer()
return self._frame_result
def _new_frame(self):
self._frame_img = None
self._geometry = None
self._barcodes = []
self._is_single_image = False
self._frame_number += 1
self._frame_result = ScanResult(self._frame_number)
self._frame_result.set_previous_plate(self._plate)
self._frame_result.start_timer()
def _perform_frame_scan(self):
self._barcodes = self._locate_all_barcodes_in_image()
self._frame_result.set_barcodes(self._barcodes)
self._geometry = self._calculate_geometry()
self._frame_result.set_geometry(self._geometry)
# Determine if the previous plate scan has any barcodes in common with this one.
has_common_barcodes, is_same_align = self._find_common_barcode(self._geometry, self._barcodes)
if has_common_barcodes and self._plate.is_full_valid():
return
elif not has_common_barcodes:
self._initialize_plate_from_barcodes()
elif has_common_barcodes and not is_same_align:
self._geometry = self._adjust_geometry(self._barcodes)
# Merge with old plate
if has_common_barcodes:
self._merge_frame_into_plate()
def _locate_all_barcodes_in_image(self):
if self._is_single_image:
# barcodes = DataMatrix.locate_all_barcodes_in_image_deep(self._frame_img, self.barcode_size)
barcodes = DataMatrix.locate_all_barcodes_in_image(self._frame_img, self.barcode_size)
else:
barcodes = DataMatrix.locate_all_barcodes_in_image(self._frame_img, self.barcode_size)
if len(barcodes) == 0:
raise NoBarcodesError("No Barcodes Detected In Image")
return barcodes
def _calculate_geometry(self):
slot_centers = [bc.center() for bc in self._barcodes]
# Use empty slots as points if not enough barcodes
if self.plate_type == Geometry.UNIPUCK:
use_emptys = len(self._barcodes) < 8
if use_emptys:
empty_circles = EmptySlotDetector.detect(self._frame_img, self._barcodes)
empty_centers = [c.center() for c in empty_circles]
slot_centers.extend(empty_centers)
geometry = Geometry.calculate_geometry(self.plate_type, slot_centers)
return geometry
def _initialize_plate_from_barcodes(self):
for bc in self._barcodes:
bc.perform_read()
if self._any_valid_barcodes():
slot_scanner = self._create_slot_scanner()
self._plate = Plate(self.plate_type)
self._plate_scan = PlateScanner(self._plate, self._is_single_image)
self._plate_scan.new_frame(self._geometry, self._barcodes, slot_scanner)
def _merge_frame_into_plate(self):
# If one of the barcodes matches the previous frame and is aligned in the same slot, then we can
# be fairly sure we are dealing with the same plate. Copy all of the barcodes that we read in the
# previous plate over to their slot in the new plate. Then read any that we haven't already read.
slot_scanner = self._create_slot_scanner()
self._plate_scan.new_frame(self._geometry, self._barcodes, slot_scanner)
def _any_valid_barcodes(self):
return any([bc.is_read() and bc.is_valid() for bc in self._barcodes])
def _create_slot_scanner(self):
slot_scanner = SlotScanner(self._frame_img, self._barcodes)
return slot_scanner
def _find_common_barcode(self, geometry, barcodes):
""" Determine if the set of finder patterns has any barcodes in common with the existing plate.
Return a boolean and a list of the barcodes that have been read. """
has_common_barcodes = False
has_common_geometry = False
num_common_barcodes = 0
# If no plate, don't bother to look for common barcodes
if self._plate is None:
return has_common_barcodes, has_common_geometry
slotted_barcodes = self._make_slotted_barcodes_list(barcodes, geometry)
# Determine if the previous plate scan has any barcodes in common with this one.
for i in range(self._plate.num_slots):
old_slot = self._plate.slot(i)
new_bc = slotted_barcodes[i-1]
# Only interested in reading barcodes that might match existing ones
if new_bc is None or old_slot.state() != Slot.VALID:
continue
# Read the barcode
new_bc.perform_read()
if not new_bc.is_valid():
continue
num_common_barcodes += 1
has_common_geometry = new_bc.data() == old_slot.barcode_data()
has_common_barcodes = has_common_geometry or self._plate.contains_barcode(new_bc.data())
# If the geometry of this and the previous frame line up, then we are done. Otherwise we
# need to read at least 2 barcodes so we can perform a realignment.
if has_common_geometry or num_common_barcodes >= 2:
break
return has_common_barcodes, has_common_geometry
@staticmethod
def _make_slotted_barcodes_list(barcodes, geometry):
# Make a list of the unread barcodes with associated slot numbers - from this frame's geometry
slotted_bcs = [None] * geometry.num_slots()
for bc in barcodes:
slot_num = geometry.containing_slot(bc.center())
slotted_bcs[slot_num - 1] = bc
return slotted_bcs
def _adjust_geometry(self, barcodes):
# If we have a barcode that matches with the previous frame but that isn't in the same slot, then
# at least one of the frames wasn't properly aligned - so we adjust the geometry to match the
# frames together
adjuster = UnipuckGeometryAdjuster()
geometry = adjuster.adjust(self._plate, barcodes)
return geometry