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Merged
Buglakova merged 3 commits into from
May 22, 2026
+113 −82
Merged

Refactor apply_transform workflow for per moving image execution #48

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b3ff079
refactor apply_transform to process one moving image per run
zh320 May 15, 2026
0c45891
split n5/dir and file apply_transform fules
zh320 May 15, 2026
f6f40d7
Merge branch 'dev' into transform
zh320 May 21, 2026
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117 changes: 56 additions & 61 deletions matchmaker/apply_transform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,22 +60,21 @@ def apply_transform(moving_img, moving_resolution, parameter_object, interpolati


@click.command()
@click.option("-mp", "--moving_paths", required=True, multiple=True, help="Paths to moving inputs")
@click.option("-mk", "--moving_keys", required=True, multiple=True, help="Keys of moving inputs")
@click.option("-mr", "--moving_resolutions", required=True, multiple=True, help="Resolutions of moving inputs")
@click.option("-op", "--output_paths", required=True, multiple=True, help="Paths to save warped images",)
@click.option("-ok", "--output_keys", required=True, multiple=True, help="Keys of moving outputs",)
@click.option("-io", "--interpolation_orders", required=True, multiple=True, help="Orders of interpolation",)
@click.option("-mp", "--moving_path", required=True, help="Path to moving input")
@click.option("-mk", "--moving_key", required=True, help="Key of moving input")
@click.option("-mr", "--moving_resolution", required=True, help="Resolution of moving input")
@click.option("-op", "--output_path", required=True, help="Path to save warped image")
@click.option("-ok", "--output_key", required=True, help="Key of moving output")
@click.option("-io", "--interpolation_order", required=True, help="Order of interpolation")
@click.option("-ld", "--log_dir", required=True, help="Log directory")
@click.option("-pm", "--parameter_map_path", required=True, help="Path to the parameter map",)
@click.option("-pt", "--prealignment_transform_path", default=None, help="Prealignment transform path",)
@click.option("-fi", "--fixed_path", default=None, help="Fixed input .n5 file")
@click.option("-fk", "--fixed_key", default=None, help="Fixed input key")
@click.option("-vb", "--verbose", is_flag=True, default=False, help="Show verbose logs")
def apply_transforms(moving_paths, moving_keys, moving_resolutions, output_paths, output_keys,
interpolation_orders, log_dir, parameter_map_path, prealignment_transform_path,
fixed_path, fixed_key, verbose):
assert len(moving_paths) == len(moving_keys) == len(moving_resolutions) == len(output_paths) == len(output_keys) == len(interpolation_orders)
def apply_transforms(moving_path, moving_key, moving_resolution, output_path, output_key,
interpolation_order, log_dir, parameter_map_path,
prealignment_transform_path, fixed_path, fixed_key, verbose):
log_dir = Path(log_dir)
log_dir.mkdir(exist_ok=True)

Expand All @@ -102,61 +101,57 @@ def apply_transforms(moving_paths, moving_keys, moving_resolutions, output_paths
logging.info("Rotate fixed image using prealignment transform")
fixed_prealigned = rotate_img(fixed_img, T_fixed, output_shape=output_shape)

for i, (moving_path, moving_key) in enumerate(zip(moving_paths, moving_keys)):
print("\n")
logging.info(f"[{i+1}/{len(moving_paths)}] Start processing moving image: {moving_path}")
moving_resolution = json.loads(moving_resolutions[i])
output_path, output_key = output_paths[i], output_keys[i]
interpolation_order = interpolation_orders[i]

moving_name = Path(moving_path).stem
logging.info("Read moving image")
moving_img = load_data(moving_path, moving_key)
if moving_path.endswith(".n5"):
if list(moving_resolution) != get_attrs(moving_path, moving_key)["resolution"]:
raise ValueError("Moving resolution from config is different from n5 file")

if moving_img.ndim == 3:
moving_img = moving_img[None, ...]
chunks = (128, 512, 512)
else:
chunks = (1, 128, 512, 512)

logging.info("Start transformation")
warped, warp_prealigned = apply_transform(moving_img,
moving_resolution,
parameter_object,
interpolation_order,
T_fixed=T_fixed,
output_shape=output_shape)

resolution = [float(res) for res in parameter_object.GetParameter(0, "Spacing")]

save_attrs = {}
if moving_path.endswith(".n5"):
attributes = dict(get_attrs(moving_path, moving_key))
attributes["resolution"] = resolution
save_attrs["chunks"] = chunks
save_attrs["attrs"] = attributes

logging.info("Plot warped image")
plot_three_slices(warped, save_path=log_dir / f"{moving_name}_warped.png")
if fixed_path:
logging.info("Plot overlay image")
plot_overlay(fixed_img, warped, log_dir / f"{moving_name}_warped_overlay.png",)
logging.info(f"Start processing moving image: {moving_path}")
moving_resolution = json.loads(moving_resolution)

if T_fixed is not None:
logging.info("Plot warped moving image after pre-alignment")
plot_three_slices(warp_prealigned, save_path=log_dir / f"{moving_name}_warp_prealigned.png")
moving_name = Path(moving_path).stem
logging.info("Read moving image")
moving_img = load_data(moving_path, moving_key)
if moving_path.endswith(".n5"):
if list(moving_resolution) != get_attrs(moving_path, moving_key)["resolution"]:
raise ValueError("Moving resolution from config is different from n5 file")

if fixed_path:
logging.info("Plot overlay image after pre-alignment")
plot_overlay(fixed_prealigned, warp_prealigned, log_dir / f"{moving_name}_warp_prealigned_overlay.png",)
if moving_img.ndim == 3:
moving_img = moving_img[None, ...]
chunks = (128, 512, 512)
else:
chunks = (1, 128, 512, 512)

logging.info("Start transformation")
warped, warp_prealigned = apply_transform(moving_img,
moving_resolution,
parameter_object,
interpolation_order,
T_fixed=T_fixed,
output_shape=output_shape)

resolution = [float(res) for res in parameter_object.GetParameter(0, "Spacing")]

save_attrs = {}
if moving_path.endswith(".n5"):
attributes = dict(get_attrs(moving_path, moving_key))
attributes["resolution"] = resolution
save_attrs["chunks"] = chunks
save_attrs["attrs"] = attributes

logging.info("Plot warped image")
plot_three_slices(warped, save_path=log_dir / f"{moving_name}_warped.png")
if fixed_path:
logging.info("Plot overlay image")
plot_overlay(fixed_img, warped, log_dir / f"{moving_name}_warped_overlay.png",)

save_data(warp_prealigned, output_path, output_key=output_key, **save_attrs)
if T_fixed is not None:
logging.info("Plot warped moving image after pre-alignment")
plot_three_slices(warp_prealigned, save_path=log_dir / f"{moving_name}_warp_prealigned.png")

else:
save_data(warped, output_path, output_key=output_key, **save_attrs)
if fixed_path:
logging.info("Plot overlay image after pre-alignment")
plot_overlay(fixed_prealigned, warp_prealigned, log_dir / f"{moving_name}_warp_prealigned_overlay.png",)

save_data(warp_prealigned, output_path, output_key=output_key, **save_attrs)

else:
save_data(warped, output_path, output_key=output_key, **save_attrs)


if __name__ == "__main__":
Expand Down
78 changes: 57 additions & 21 deletions workflows/apply_transform.smk
View file
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import json
import re

configfile: "examples/register_config_test_rigid_apply_transform.yaml"

Expand All @@ -18,9 +19,9 @@ prealignment_transform_path = config["prealignment_transform_path"]
fixed_path = config["fixed_image"]["input_path"]
fixed_key = config["fixed_image"]["input_key"]


def expand_flag(flag, values):
return " ".join(f"{flag} {v}" for v in values)
TARGET_OUTPUTS = [f"{p}/{k}" if p.endswith(".n5") else p for p, k in zip(output_paths, output_keys)]
FILE_OUTPUTS = [p for p in TARGET_OUTPUTS if not ".n5/" in p]
N5_OUTPUTS = [p for p in TARGET_OUTPUTS if ".n5/" in p]


def get_all_opts(d):
Expand All @@ -33,41 +34,76 @@ def get_all_opts(d):

rule all:
input:
output_paths,
TARGET_OUTPUTS,


rule apply_transform:
rule apply_transform_file:
input:
parameter_map_path = parameter_map_path,
moving_img = lambda w: moving_paths[TARGET_OUTPUTS.index(w.out_file)]
output:
[directory(f"{path}/{key}") if path.endswith(".n5") else path for path, key in zip(output_paths, output_keys)],
out_file = "{out_file}"
wildcard_constraints:
out_file = "^(" + "|".join(re.escape(p) for p in FILE_OUTPUTS) + ")$" if FILE_OUTPUTS else "$^"
params:
opts = lambda w: get_all_opts({
"prealignment_transform_path": prealignment_transform_path,
"fixed_path": fixed_path,
"fixed_key": fixed_key,
}),
moving_path = lambda w: moving_paths[TARGET_OUTPUTS.index(w.out_file)],
moving_key = lambda w: moving_keys[TARGET_OUTPUTS.index(w.out_file)],
moving_resolution = lambda w: moving_resolutions[TARGET_OUTPUTS.index(w.out_file)],
output_path = lambda w: output_paths[TARGET_OUTPUTS.index(w.out_file)],
output_key = lambda w: output_keys[TARGET_OUTPUTS.index(w.out_file)],
interpolation_order = lambda w: interpolation_orders[TARGET_OUTPUTS.index(w.out_file)],
conda: "matchmaker_env"
shell:
"""
python matchmaker/apply_transform.py \
{params.opts} \
--moving_path {params.moving_path} \
--moving_key {params.moving_key} \
--moving_resolution '{params.moving_resolution}' \
--output_path {params.output_path} \
--output_key {params.output_key} \
--interpolation_order {params.interpolation_order} \
--log_dir {log_dir} \
--parameter_map_path {input.parameter_map_path}
"""

moving_paths = expand_flag("--moving_paths", moving_paths),
moving_keys = expand_flag("--moving_keys", moving_keys),
moving_resolutions = expand_flag("--moving_resolutions", moving_resolutions),
output_paths = expand_flag("--output_paths", output_paths),
output_keys = expand_flag("--output_keys", output_keys),
interpolation_orders = expand_flag("--interpolation_orders", interpolation_orders),
log_dir = log_dir,

log: f"{log_dir}/matchmaker.log"
rule apply_transform_n5:
input:
parameter_map_path = parameter_map_path,
moving_img = lambda w: moving_paths[TARGET_OUTPUTS.index(w.out_dir)]
output:
out_dir = directory("{out_dir}")
wildcard_constraints:
out_dir = "^(" + "|".join(re.escape(p) for p in N5_OUTPUTS) + ")$" if N5_OUTPUTS else "$^"
params:
opts = lambda w: get_all_opts({
"prealignment_transform_path": prealignment_transform_path,
"fixed_path": fixed_path,
"fixed_key": fixed_key,
}),
moving_path = lambda w: moving_paths[TARGET_OUTPUTS.index(w.out_dir)],
moving_key = lambda w: moving_keys[TARGET_OUTPUTS.index(w.out_dir)],
moving_resolution = lambda w: moving_resolutions[TARGET_OUTPUTS.index(w.out_dir)],
output_path = lambda w: output_paths[TARGET_OUTPUTS.index(w.out_dir)],
output_key = lambda w: output_keys[TARGET_OUTPUTS.index(w.out_dir)],
interpolation_order = lambda w: interpolation_orders[TARGET_OUTPUTS.index(w.out_dir)],
conda: "matchmaker_env"
shell:
"""
python matchmaker/apply_transform.py \
{params.opts} \
{params.moving_paths} \
{params.moving_keys} \
{params.moving_resolutions} \
{params.output_paths} \
{params.output_keys} \
{params.interpolation_orders} \
--log_dir {params.log_dir} \
--moving_path {params.moving_path} \
--moving_key {params.moving_key} \
--moving_resolution '{params.moving_resolution}' \
--output_path {params.output_path} \
--output_key {params.output_key} \
--interpolation_order {params.interpolation_order} \
--log_dir {log_dir} \
--parameter_map_path {input.parameter_map_path}
"""