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David Rotermund 2024-02-26 14:38:19 +01:00 committed by GitHub
parent 4173e3306e
commit e462ea94c5
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1 changed files with 10 additions and 3 deletions
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13
new_pipeline/stage_2_make_heartbeat_mask.py
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@ -20,17 +20,24 @@ mylogger.info("loading config file")
with open("config.json", "r") as file: with open("config.json", "r") as file:
config = json.loads(jsmin(file.read())) config = json.loads(jsmin(file.read()))
threshold: float = 0.05
path: str = config["ref_image_path"] path: str = config["ref_image_path"]
use_channel: str = "donor" use_channel: str = "donor"
spatial_width: float = 4.0 spatial_width: float = 4.0
temporal_width: float = 0.1 temporal_width: float = 0.1
threshold: float = 0.05
heartbeat_mask_threshold_file: str = os.path.join(path, "heartbeat_mask_threshold.npy")
if os.path.isfile(heartbeat_mask_threshold_file):
mylogger.info(f"loading previous threshold file: {heartbeat_mask_threshold_file}")
threshold = float(np.load(heartbeat_mask_threshold_file)[0])
mylogger.info(f"initial threshold is {threshold}")
image_ref_file: str = os.path.join(path, use_channel + ".npy") image_ref_file: str = os.path.join(path, use_channel + ".npy")
image_var_file: str = os.path.join(path, use_channel + "_var.npy") image_var_file: str = os.path.join(path, use_channel + "_var.npy")
heartbeat_mask_file: str = os.path.join(path, "heartbeat_mask.npy") heartbeat_mask_file: str = os.path.join(path, "heartbeat_mask.npy")
heartbeat_mask_threshold_file: str = os.path.join(path, "heartbeat_mask_threshold.npy")
device = get_torch_device(mylogger, config["force_to_cpu"]) device = get_torch_device(mylogger, config["force_to_cpu"])
@ -124,7 +131,7 @@ mylogger.info("Add controls")
axfreq = fig.add_axes(rect=(0.4, 0.9, 0.3, 0.03)) axfreq = fig.add_axes(rect=(0.4, 0.9, 0.3, 0.03))
slice_slider = Slider( slice_slider = Slider(
ax=axfreq, ax=axfreq,
label="Slice", label="Threshold",
valmin=0, valmin=0,
valmax=value_sort_max, valmax=value_sort_max,
valinit=threshold, valinit=threshold,