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add interest point registration #56

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merged 1 commit into from
Oct 27, 2024
Merged

add interest point registration #56

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8 changes: 8 additions & 0 deletions config/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,14 @@ basic_flatfield_corr:


bigstitcher:
use_interestpoints: False
interest_points:
downsample_xy: 4
min_intensity: 0
max_intensity: 2000
label: beads
threshold: 0.008
sigma: 1.8
calc_pairwise_shifts:
downsample_in_x: 4
downsample_in_y: 4
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149 changes: 143 additions & 6 deletions workflow/rules/bigstitcher.smk
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Expand Up @@ -163,15 +163,152 @@ rule bigstitcher_stitching:
"{params.rm_old_xml}"


rule bigstitcher_detect_interestpoints:
input:
dataset_n5=rules.zarr_to_bdv.output.bdv_n5,
dataset_xml=rules.zarr_to_bdv.output.bdv_xml,
params:
downsampling="--downsampleXY={dsxy}".format(
dsxy=config["bigstitcher"]["interest_points"]["downsample_xy"],
),
min_intensity="--minIntensity={min_intensity}".format(
min_intensity=config["bigstitcher"]["interest_points"]["min_intensity"]
),
max_intensity="--maxIntensity={max_intensity}".format(
max_intensity=config["bigstitcher"]["interest_points"]["max_intensity"]
),
label="--label={label}".format(
label=config["bigstitcher"]["interest_points"]["label"]
),
threshold="--threshold={threshold}".format(
threshold=config["bigstitcher"]["interest_points"]["threshold"]
),
sigma="--sigma={sigma}".format(
sigma=config["bigstitcher"]["interest_points"]["sigma"]
),
mem_gb=lambda wildcards, resources: "{mem_gb}".format(
mem_gb=int(resources.mem_mb / 1000)
),
rm_old_xml=lambda wildcards, output: f"rm -f {output.dataset_xml}~?",
output:
dataset_xml=temp(
bids(
root=work,
subject="{subject}",
datatype="micr",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="bigstitcherdetectinterestpoints.xml",
)
),
benchmark:
bids(
root="benchmarks",
datatype="bigstitcherdetectinterestpoints",
subject="{subject}",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="benchmark.tsv",
)
log:
bids(
root="logs",
datatype="bigstitcherdetectinterestpoints",
subject="{subject}",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="log.txt",
),
container:
config["containers"]["spimprep"]
resources:
runtime=30,
mem_mb=int(config["total_mem_mb"] * 0.9),
threads: config["total_cores"]
group:
"preproc"
shell:
"cp {input.dataset_xml} {output.dataset_xml} && "
"detect-interestpoints {params.mem_gb} {threads} -x {output.dataset_xml} "
" {params.min_intensity} {params.max_intensity} {params.downsampling} "
" {params.sigma} {params.threshold} {params.label} && "
"{params.rm_old_xml}"


rule bigstitcher_match_interestpoints:
input:
dataset_n5=rules.zarr_to_bdv.output.bdv_n5,
dataset_xml=rules.bigstitcher_detect_interestpoints.output.dataset_xml,
params:
label="--label={label}".format(label="beads"),
method="--method={method}".format(method="ICP"),
mem_gb=lambda wildcards, resources: "{mem_gb}".format(
mem_gb=int(resources.mem_mb / 1000)
),
rm_old_xml=lambda wildcards, output: f"rm -f {output.dataset_xml}~?",
output:
dataset_xml=temp(
bids(
root=work,
subject="{subject}",
datatype="micr",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="bigstitchermatchinterestpoints.xml",
)
),
benchmark:
bids(
root="benchmarks",
datatype="bigstitchermatchinterestpoints",
subject="{subject}",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="benchmark.tsv",
)
log:
bids(
root="logs",
datatype="bigstitchermatchinterestpoints",
subject="{subject}",
sample="{sample}",
acq="{acq}",
desc="{desc}",
suffix="log.txt",
),
container:
config["containers"]["spimprep"]
resources:
runtime=30,
mem_mb=int(config["total_mem_mb"] * 0.9),
threads: config["total_cores"]
group:
"preproc"
shell:
"cp {input.dataset_xml} {output.dataset_xml} && "
"match-interestpoints {params.mem_gb} {threads} -x {output.dataset_xml} "
" {params.method} {params.label} && "
"{params.rm_old_xml}"


rule bigstitcher_solver:
input:
dataset_n5=rules.zarr_to_bdv.output.bdv_n5,
dataset_xml=rules.bigstitcher_stitching.output.dataset_xml,
dataset_xml=(
rules.bigstitcher_match_interestpoints.output.dataset_xml
if config["bigstitcher"]["use_interestpoints"]
else rules.bigstitcher_stitching.output.dataset_xml
),
params:
downsampling="--downsampling={dsx},{dsy},{dsz}".format(
dsx=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_x"],
dsy=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_y"],
dsz=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_z"],
label="--label={label}".format(label="beads"),
lambdareg="--lambda={lambdareg}".format(lambdareg=0.1),
source="-s {source}".format(
source="IP" if config["bigstitcher"]["use_interestpoints"] else "STITCHING"
),
method="--method={method}".format(
method=config["bigstitcher"]["global_optimization"]["method"]
Expand Down Expand Up @@ -223,7 +360,7 @@ rule bigstitcher_solver:
shell:
"cp {input.dataset_xml} {output.dataset_xml} && "
"solver {params.mem_gb} {threads} -x {output.dataset_xml} "
" -s STITCHING --lambda 0.1 "
" {params.source} {params.label} {params.lambdareg}"
" {params.method} && "
"{params.rm_old_xml}"

Expand Down