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add round registration that uses all channels

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This commit is contained in:
Hannes F. Kuchelmeister
2021-07-21 18:31:40 +02:00
parent 53261f9ae1
commit 60d7166c5b
2 changed files with 34 additions and 1 deletions
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2
situr/registration/__init__.py
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@@ -1,5 +1,5 @@
from .registration import Registration, RegistrationFunction, FilterregRegistrationFunction
from .channel_registration import ChannelRegistration
from .round_registration import RoundRegistration
from .round_registration import RoundRegistration, AllChannelRoundRegistration
from .tile_registration import CombinedRegistration
from .peak_finder import PeakFinder, PeakFinderDifferenceOfGaussian

33
situr/registration/round_registration.py
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@@ -1,5 +1,6 @@
from situr.registration import Registration, RegistrationFunction, FilterregRegistrationFunction
import numpy as np
class RoundRegistration(Registration):
@@ -22,3 +23,35 @@ class RoundRegistration(Registration):
transformation = self.registration_function.do_registration(
current_round_peaks, reference_peaks)
situ_tile.set_round_transformation(round, transformation)
class AllChannelRoundRegistration(RoundRegistration):
def do_round_registration(self, situ_tile, reference_round: int = 0, reference_channel: int = 0):
"""This method generates a round registration transformation for a tile and saves it in the tile.
Args:
situ_tile (Tile): The tile that the transformation is to be performed on.
reference_round (int, optional): The round that is referenced and will not be changed. Defaults to 0.
reference_channel (int, optional): This parameter is ignored.
"""
reference_peaks = []
for channel in range(situ_tile.get_channel_count()):
# TODO: possibly exclude nucleaus channel
reference_peaks.append(self.peak_finder.get_channel_peaks(situ_tile.get_round(
reference_round), channel))
reference_peaks = np.concatenate(reference_peaks, axis=0)
for round in range(situ_tile.get_round_count()):
if round != reference_channel:
current_round_peaks = []
for channel in range(situ_tile.get_channel_count()):
# TODO: possibly exclude nucleaus channel
current_round_peaks.append(self.peak_finder.get_channel_peaks(
situ_tile.get_round(round), channel))
current_round_peaks = np.concatenate(
current_round_peaks, axis=0)
transformation = self.registration_function.do_registration(
current_round_peaks, reference_peaks)
situ_tile.set_round_transformation(round, transformation)