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added optional params cp_path and logfile_name to the setup_logger fu… #862

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Merged
carsen-stringer merged 3 commits into from
Sep 7, 2024
Merged

added optional params cp_path and logfile_name to the setup_logger fu… #862

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43153f0
added optional params cp_path and logfile_name to the setup_logger fu…
Feb 16, 2024
6717531
Merge branch 'main' into set-custom-log-path
carsen-stringer Sep 7, 2024
5f2f541
Update io.py
carsen-stringer Sep 7, 2024
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20 changes: 7 additions & 13 deletions cellpose/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,11 +47,10 @@

io_logger = logging.getLogger(__name__)


def logger_setup():
cp_dir = pathlib.Path.home().joinpath(".cellpose")
def logger_setup(cp_path=".cellpose", logfile_name="run.log"):
cp_dir = pathlib.Path.home().joinpath(cp_path)
cp_dir.mkdir(exist_ok=True)
log_file = cp_dir.joinpath("run.log")
log_file = cp_dir.joinpath(logfile_name)
try:
log_file.unlink()
except:
Expand All @@ -70,8 +69,7 @@ def logger_setup():

from . import utils, plot, transforms


# helper function to check for a path; if it doesn"t exist, make it
# helper function to check for a path; if it doesn't exist, make it
def check_dir(path):
if not os.path.isdir(path):
os.mkdir(path)
Expand Down Expand Up @@ -338,7 +336,6 @@ def get_image_files(folder, mask_filter, imf=None, look_one_level_down=False):

return image_names


def get_label_files(image_names, mask_filter, imf=None):
"""
Get the label files corresponding to the given image names and mask filter.
Expand Down Expand Up @@ -440,7 +437,6 @@ def load_images_labels(tdir, mask_filter="_masks", image_filter=None,
io_logger.info(f"{k} / {nimg} images in {tdir} folder have labels")
return images, labels, image_names


def load_train_test_data(train_dir, test_dir=None, image_filter=None,
mask_filter="_masks", look_one_level_down=False):
"""
Expand All @@ -463,7 +459,6 @@ def load_train_test_data(train_dir, test_dir=None, image_filter=None,
"""
images, labels, image_names = load_images_labels(train_dir, mask_filter,
image_filter, look_one_level_down)

# testing data
test_images, test_labels, test_image_names = None, None, None
if test_dir is not None:
Expand Down Expand Up @@ -568,12 +563,11 @@ def masks_flows_to_seg(images, masks, flows, file_names, diams=30., channels=Non

np.save(base + "_seg.npy", dat)


def save_to_png(images, masks, flows, file_names):
""" deprecated (runs io.save_masks with png=True)
""" deprecated (runs io.save_masks with png=True)

does not work for 3D images

"""
save_masks(images, masks, flows, file_names, png=True)

Expand Down