davrot/gevi
1
0
Fork 0
mirror of https://github.com/davrot/gevi.git synced 2025-04-20 22:26:43 +02:00
Code Issues Projects Releases Packages Wiki Activity Actions

Delete stage_3_refine_mask.py

Browse source
This commit is contained in:
David Rotermund 2025-03-19 18:29:29 +01:00 • committed by GitHub
parent 580a85b964
commit a3fe0e9d5f
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
1 changed files with 0 additions and 169 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

169
stage_3_refine_mask.py
View file

@ -1,169 +0,0 @@
import os
import numpy as np
import matplotlib.pyplot as plt # type:ignore
import matplotlib
from matplotlib.widgets import Button # type:ignore
# pip install roipoly
from roipoly import RoiPoly # type:ignore
from functions.create_logger import create_logger
from functions.load_config import load_config
import argh
def compose_image(image_3color: np.ndarray, mask: np.ndarray) -> np.ndarray:
display_image = image_3color.copy()
display_image[..., 2] = display_image[..., 0]
display_image[mask == 0, :] = 1.0
return display_image
def main(*, config_filename: str = "config.json") -> None:
mylogger = create_logger(
save_logging_messages=True,
display_logging_messages=True,
log_stage_name="stage_3",
)
config = load_config(mylogger=mylogger, filename=config_filename)
path: str = config["ref_image_path"]
use_channel: str = "donor"
padding: int = 20
image_ref_file: str = os.path.join(path, use_channel + ".npy")
heartbeat_mask_file: str = os.path.join(path, "heartbeat_mask.npy")
refined_mask_file: str = os.path.join(path, "mask_not_rotated.npy")
mylogger.info(f"loading image reference file: {image_ref_file}")
image_ref: np.ndarray = np.load(image_ref_file)
image_ref /= image_ref.max()
image_ref = np.pad(image_ref, pad_width=padding)
mylogger.info(f"loading heartbeat mask: {heartbeat_mask_file}")
mask: np.ndarray = np.load(heartbeat_mask_file)
mask = np.pad(mask, pad_width=padding)
image_3color = np.concatenate(
(
np.zeros_like(image_ref[..., np.newaxis]),
image_ref[..., np.newaxis],
np.zeros_like(image_ref[..., np.newaxis]),
),
axis=-1,
)
mylogger.info("-==- DONE -==-")
fig, ax_main = plt.subplots()
display_image = compose_image(image_3color=image_3color, mask=mask)
image_handle = ax_main.imshow(display_image, vmin=0, vmax=1, cmap="hot")
mylogger.info("Add controls")
def on_clicked_accept(event: matplotlib.backend_bases.MouseEvent) -> None:
nonlocal mylogger
nonlocal refined_mask_file
nonlocal mask
mylogger.info(f"Save mask to: {refined_mask_file}")
mask = mask[padding:-padding, padding:-padding]
np.save(refined_mask_file, mask)
exit()
def on_clicked_cancel(event: matplotlib.backend_bases.MouseEvent) -> None:
nonlocal mylogger
mylogger.info("Ended without saving the mask")
exit()
def on_clicked_add(event: matplotlib.backend_bases.MouseEvent) -> None:
nonlocal new_roi # type: ignore
nonlocal mask
nonlocal image_3color
nonlocal display_image
nonlocal mylogger
if len(new_roi.x) > 0:
mylogger.info(
"A ROI with the following coordiantes has been added to the mask"
)
for i in range(0, len(new_roi.x)):
mylogger.info(f"{round(new_roi.x[i], 1)} x {round(new_roi.y[i], 1)}")
mylogger.info("")
new_mask = new_roi.get_mask(display_image[:, :, 0])
mask[new_mask] = 0.0
display_image = compose_image(image_3color=image_3color, mask=mask)
image_handle.set_data(display_image)
for line in ax_main.lines:
line.remove()
plt.draw()
new_roi = RoiPoly(ax=ax_main, color="r", close_fig=False, show_fig=False)
def on_clicked_remove(event: matplotlib.backend_bases.MouseEvent) -> None:
nonlocal new_roi # type: ignore
nonlocal mask
nonlocal image_3color
nonlocal display_image
if len(new_roi.x) > 0:
mylogger.info(
"A ROI with the following coordiantes has been removed from the mask"
)
for i in range(0, len(new_roi.x)):
mylogger.info(f"{round(new_roi.x[i], 1)} x {round(new_roi.y[i], 1)}")
mylogger.info("")
new_mask = new_roi.get_mask(display_image[:, :, 0])
mask[new_mask] = 1.0
display_image = compose_image(image_3color=image_3color, mask=mask)
image_handle.set_data(display_image)
for line in ax_main.lines:
line.remove()
plt.draw()
new_roi = RoiPoly(ax=ax_main, color="r", close_fig=False, show_fig=False)
axbutton_accept = fig.add_axes(rect=(0.3, 0.85, 0.2, 0.04))
button_accept = Button(
ax=axbutton_accept, label="Accept", image=None, color="0.85", hovercolor="0.95"
)
button_accept.on_clicked(on_clicked_accept) # type: ignore
axbutton_cancel = fig.add_axes(rect=(0.5, 0.85, 0.2, 0.04))
button_cancel = Button(
ax=axbutton_cancel, label="Cancel", image=None, color="0.85", hovercolor="0.95"
)
button_cancel.on_clicked(on_clicked_cancel) # type: ignore
axbutton_addmask = fig.add_axes(rect=(0.3, 0.9, 0.2, 0.04))
button_addmask = Button(
ax=axbutton_addmask,
label="Add mask",
image=None,
color="0.85",
hovercolor="0.95",
)
button_addmask.on_clicked(on_clicked_add) # type: ignore
axbutton_removemask = fig.add_axes(rect=(0.5, 0.9, 0.2, 0.04))
button_removemask = Button(
ax=axbutton_removemask,
label="Remove mask",
image=None,
color="0.85",
hovercolor="0.95",
)
button_removemask.on_clicked(on_clicked_remove) # type: ignore
# ax_main.cla()
mylogger.info("Display")
new_roi: RoiPoly = RoiPoly(ax=ax_main, color="r", close_fig=False, show_fig=False)
plt.show()
if __name__ == "__main__":
argh.dispatch_command(main)