153 lines
6.0 KiB
Python
153 lines
6.0 KiB
Python
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from CellData import CellData, icelldata_of_dir
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from os import listdir
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import os
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def main():
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# choose_thresholds()
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precalculate_baseline_spiketimes()
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def precalculate_baseline_spiketimes():
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threshold_file_path = "data/thresholds.tsv"
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thresholds_dict = {}
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if os.path.exists(threshold_file_path):
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with open(threshold_file_path, "r") as threshold_file:
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for line in threshold_file:
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line = line.strip()
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line = line.split('\t')
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name = line[0]
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thresh = float(line[1])
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min_length = int(line[2])
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step_size = int(line[3])
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thresholds_dict[name] = [thresh, min_length, step_size]
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for cell_data in icelldata_of_dir("data/final/"):
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name = os.path.basename(cell_data.get_data_path())
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if name not in thresholds_dict.keys():
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print("key missing: {}".format(name))
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continue
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thresh = thresholds_dict[name][0]
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min_length = thresholds_dict[name][1]
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split_step_size = thresholds_dict[name][2]
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cell_data.get_base_spikes(threshold=thresh, min_length=min_length, split_step=split_step_size)
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def choose_thresholds():
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base_path = "data/final/"
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threshold_file_path = "data/thresholds.tsv"
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re_choose_thresholds = False
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thresholds_dict = {}
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if os.path.exists(threshold_file_path):
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with open(threshold_file_path, "r") as threshold_file:
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for line in threshold_file:
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line = line.strip()
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line = line.split('\t')
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name = line[0]
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thresh = float(line[1])
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if len(line) > 2:
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min_length = int(line[2])
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step_size = int(line[3])
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thresholds_dict[name] = [thresh, min_length, step_size]
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print("Already done:", name)
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else:
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thresholds_dict[name] = [thresh]
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print("Already done (no len/step): ", name)
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count = 0
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for item in sorted(listdir(base_path)):
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if item in thresholds_dict.keys() and thresholds_dict[item][0] != 99 and not re_choose_thresholds:
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continue
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count += 1
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print("cells to do:", count)
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for item in sorted(listdir(base_path)):
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# starting assumptions:
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thresh = 2.5
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min_split_length = 5000
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split_step_size = 1000
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if "thresholds" in item:
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continue
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if item in thresholds_dict.keys() and thresholds_dict[item][0] != 99 and not re_choose_thresholds:
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if len(thresholds_dict[item]) == 1:
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thresholds_dict[item] = [thresholds_dict[item][0], min_split_length, split_step_size]
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continue
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print(item)
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item_path = base_path + item
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data = CellData(item_path)
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trace = data.get_base_traces(trace_type=data.V1)
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if len(trace) == 0:
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print("NO V1 TRACE FOUND: ", item_path)
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continue
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data.get_base_spikes(thresh, min_length=min_split_length, split_step=split_step_size, re_calculate=True,
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only_first=True)
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stop = False
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print("Threshold was {:.2f}, Min Length was {:.0f}, Split step size was {:.0f}".format(thresh, min_split_length,
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split_step_size))
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response = input(
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"Choose: 'ok', 'stop', or a number (threshold) or three numbers (threshold, minlength, step_size) seperated with commas")
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while response != "ok":
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if response == "stop":
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stop = True
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break
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try:
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parts = response.split(",")
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if len(parts) == 1:
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thresh = float(response)
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else:
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thresh = float(parts[0])
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min_split_length = int(parts[1])
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split_step_size = int(parts[2])
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except ValueError as e:
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print("{} could not be parsed as number or ok please try again.".format(response))
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print("Threshold was {:.2f}, Min Length was {:.0f}, Split step size was {:.0f}".format(thresh,
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min_split_length,
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split_step_size))
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response = input(
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"Choose: 'ok', 'stop', or a number (threshold) or three numbers (threshold, minlength, step_size) seperated with commas")
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continue
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data.get_base_spikes(thresh, min_length=min_split_length, split_step=split_step_size, re_calculate=True,
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only_first=True)
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print(
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"Threshold was {:.2f}, Min Length was {:.0f}, Split step size was {:.0f}".format(thresh,
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min_split_length,
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split_step_size))
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response = input(
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"Choose: 'ok', 'stop', or a number (threshold) or three numbers (threshold, minlength, step_size) seperated with commas")
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if stop:
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break
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thresholds_dict[item] = [thresh, min_split_length, split_step_size]
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with open(threshold_file_path, "w") as threshold_file:
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for name in sorted(thresholds_dict.keys()):
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if len(thresholds_dict[name]) == 1:
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threshold_file.write(name + "\t" + str(thresholds_dict[name][0]) + "\n")
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else:
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line = name + "\t"
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line += str(thresholds_dict[name][0]) + "\t"
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line += str(thresholds_dict[name][1]) + "\t"
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line += str(thresholds_dict[name][2]) + "\n"
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threshold_file.write(line)
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if __name__ == '__main__':
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main()
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