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added logging #160

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merged 4 commits into from
Jan 16, 2022
Merged

added logging #160

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bf4401f
added logging
akhanf Jan 15, 2022
e1519fe
formatting
akhanf Jan 16, 2022
712fd2a
fixes for report generation
akhanf Jan 16, 2022
008aa16
formatting
akhanf Jan 16, 2022
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11 changes: 5 additions & 6 deletions hippunfold/workflow/rules/autotop.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ import os
import numpy as np


def get_cmd_laplace_coords(wildcards):
def get_cmd_laplace_coords():
if config["skip_inject_template_labels"]:
cmd = "../scripts/laplace_coords.py"
else:
Expand Down Expand Up @@ -50,7 +50,6 @@ rule laplace_coords_hipp:
input:
unpack(get_inputs_laplace),
params:
cmd=get_cmd_laplace_coords,
gm_labels=lambda wildcards: config["laplace_labels"][wildcards.dir]["gm"],
src_labels=lambda wildcards: config["laplace_labels"][wildcards.dir]["src"],
sink_labels=lambda wildcards: config["laplace_labels"][wildcards.dir]["sink"],
Expand Down Expand Up @@ -81,7 +80,7 @@ rule laplace_coords_hipp:
suffix="laplace-hipp.txt"
),
script:
"{params.cmd}"
get_cmd_laplace_coords()


rule laplace_coords_dentate:
Expand Down Expand Up @@ -188,7 +187,7 @@ rule equivolume_coords:
**config["subj_wildcards"]
),
params:
src_labels=lambda wildcards: config["laplace_labels"][wildcards.dir]["src"],
script=os.path.join(workflow.basedir, "scripts/equivolume_coords.py"),
output:
coords=bids(
root=work,
Expand All @@ -215,8 +214,8 @@ rule equivolume_coords:
),
container:
config["singularity"]["autotop"]
script:
"../scripts/equivolume_coords.py"
shell:
"python {params.script} {resources.tmpdir} {input.innerbin} {input.outerbin} {output.coords} &> {log}"


rule unflip_coords:
Expand Down
2 changes: 1 addition & 1 deletion hippunfold/workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -378,7 +378,7 @@ rule archive_work_after_final:
"subj"
shell:
#exit code 0 or 1 is acceptable (2 is fatal)
"tar -cvzf {output} {params.work_dir}; "
"tar -czf {output} {params.work_dir}; "
"if [ $? -le 1 ]; then "
" rm -rf {params.work_dir}; "
"else exit 1; "
Expand Down
32 changes: 31 additions & 1 deletion hippunfold/workflow/rules/gifti.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,16 @@ rule constrain_surf_to_bbox:
label="{autotop}",
**config["subj_wildcards"]
),
log:
bids(
root="logs",
den="{density}",
suffix="{surfname}.txt",
desc="constrainbbox",
hemi="{hemi}",
label="{autotop}",
**config["subj_wildcards"]
),
group:
"subj"
script:
Expand Down Expand Up @@ -412,13 +422,23 @@ rule calculate_gyrification:
label="{autotop}",
**config["subj_wildcards"]
),
log:
bids(
root="logs",
den="{density}",
suffix="calcgyrification.txt",
space="{space}",
hemi="{hemi}",
label="{autotop}",
**config["subj_wildcards"]
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
'wb_command -metric-math "nativearea/unfoldarea" {output.gii}'
" -var nativearea {input.native_surfarea} -var unfoldarea {input.unfold_surfarea}"
" -var nativearea {input.native_surfarea} -var unfoldarea {input.unfold_surfarea} &> {log}"


rule smooth_surface:
Expand Down Expand Up @@ -559,6 +579,16 @@ rule resample_bigbrain_subfield_label_gii:
label="hipp",
**config["subj_wildcards"]
),
log:
bids(
root="logs",
den="{density}",
suffix="resamplesubfieldsurf",
space="{space}",
hemi="{hemi}",
label="hipp",
**config["subj_wildcards"]
),
group:
"subj"
script:
Expand Down
29 changes: 23 additions & 6 deletions hippunfold/workflow/rules/nnunet.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -109,6 +109,14 @@ rule run_inference:
space="corobl",
hemi="{hemi,Lflip|R}"
),
log:
bids(
root="logs",
**config["subj_wildcards"],
suffix="nnunet.txt",
space="corobl",
hemi="{hemi,Lflip|R}"
),
shadow:
"minimal"
threads: 16
Expand All @@ -127,12 +135,12 @@ rule run_inference:
# run inference
#copy from temp output folder to final output
"mkdir -p {params.model_dir} {params.in_folder} {params.out_folder} && "
"cp -v {input.in_img} {params.temp_img} && "
"tar -xvf {input.model_tar} -C {params.model_dir} && "
"cp {input.in_img} {params.temp_img} && "
"tar -xf {input.model_tar} -C {params.model_dir} && "
"export RESULTS_FOLDER={params.model_dir} && "
"export nnUNet_n_proc_DA={threads} && "
"nnUNet_predict -i {params.in_folder} -o {params.out_folder} -t {params.task} -chk {params.chkpnt} {params.disable_tta} && "
"cp -v {params.temp_lbl} {output.nnunet_seg}"
"nnUNet_predict -i {params.in_folder} -o {params.out_folder} -t {params.task} -chk {params.chkpnt} {params.disable_tta} &> {log} && "
"cp {params.temp_lbl} {output.nnunet_seg}"


rule unflip_nnunet_nii:
Expand Down Expand Up @@ -230,11 +238,20 @@ rule qc_nnunet_f3d:
),
container:
config["singularity"]["autotop"]
log:
bids(
root="logs",
**config["subj_wildcards"],
suffix="qcreg.txt",
desc="f3d",
space="corobl",
hemi="{hemi}"
),
group:
"subj"
shell:
"reg_f3d -flo {input.img} -ref {input.ref} -res {output.res} -cpp {output.cpp} && "
"reg_resample -flo {input.seg} -cpp {output.cpp} -ref {input.ref} -res {output.res_mask} -inter 0"
"reg_f3d -flo {input.img} -ref {input.ref} -res {output.res} -cpp {output.cpp} &> {log} && "
"reg_resample -flo {input.seg} -cpp {output.cpp} -ref {input.ref} -res {output.res_mask} -inter 0 &> {log}"


rule qc_nnunet_dice:
Expand Down
34 changes: 0 additions & 34 deletions hippunfold/workflow/rules/preproc_t1.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -123,40 +123,6 @@ rule reg_to_template:
"{params.cmd}"


rule qc_reg_to_template:
input:
ref=lambda wildcards: os.path.join(
workflow.basedir,
"..",
config["template_files"][config["template"]][wildcards.native_modality],
),
flo=bids(
root=work,
datatype="anat",
**config["subj_wildcards"],
suffix="{native_modality}.nii.gz",
space=config["template"],
desc="affine"
),
output:
png=report(
bids(
root=root,
datatype="qc",
**config["subj_wildcards"],
suffix="regqc.png",
from_="{native_modality}",
to=config["template"]
),
caption="../report/t1w_template_regqc.rst",
category="Registration QC",
),
group:
"subj"
script:
"../scripts/vis_regqc.py"


rule convert_template_xfm_ras2itk:
input:
bids(
Expand Down
24 changes: 22 additions & 2 deletions hippunfold/workflow/rules/preproc_t2.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -231,12 +231,22 @@ rule reg_t2_to_t1:
desc="rigid",
type_="itk"
),
log:
bids(
root="logs",
**config["subj_wildcards"],
suffix="reg.txt",
from_="T2w",
to="T1w",
desc="rigid",
type_="ras"
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac && "
"reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac &> {log} && "
"c3d_affine_tool {output.xfm_ras} -oitk {output.xfm_itk}"


Expand Down Expand Up @@ -275,12 +285,22 @@ rule reg_t2_to_template:
desc="affine",
type_="ras"
),
log:
bids(
root="logs",
**config["subj_wildcards"],
suffix="reg.txt",
from_="T2w",
to=config["template"],
desc="affine",
type_="ras"
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"{params.cmd}"
"{params.cmd}" + " &> {log}"


def get_inputs_compose_t2_xfm_corobl(wildcards):
Expand Down
35 changes: 34 additions & 1 deletion hippunfold/workflow/rules/qc.smk
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Original file line number Diff line number Diff line change
@@ -1,3 +1,36 @@
rule qc_reg_to_template:
input:
ref=lambda wildcards: os.path.join(
workflow.basedir,
"..",
config["template_files"][config["template"]][wildcards.native_modality],
),
flo=bids(
root=work,
datatype="anat",
**config["subj_wildcards"],
suffix="{native_modality}.nii.gz",
space=config["template"],
desc="affine"
),
output:
png=report(
bids(
root=root,
datatype="qc",
**config["subj_wildcards"],
suffix="regqc.png",
from_="{native_modality}",
to=config["template"]
),
caption="../report/t1w_template_regqc.rst",
category="Registration QC",
),
group:
"subj"
script:
"../scripts/vis_regqc.py"


rule get_subfield_vols_subj:
"""Export segmentation volume for a subject to TSV"""
Expand Down Expand Up @@ -127,7 +160,7 @@ rule qc_subfield:
output:
png=report(
bids(
root=work,
root=root,
datatype="qc",
suffix="dseg.png",
desc="subfields",
Expand Down
22 changes: 19 additions & 3 deletions hippunfold/workflow/rules/shape_inject.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,6 @@ rule template_shape_reg:
bids(
root="logs",
**config["subj_wildcards"],
space="corobl",
hemi="{hemi,Lflip|R}",
suffix="templateshapereg.txt"
),
Expand Down Expand Up @@ -260,13 +259,20 @@ rule template_shape_inject:
space="corobl",
hemi="{hemi,Lflip|R}"
),
log:
bids(
root="logs",
**config["subj_wildcards"],
suffix="templateshapeinject.txt",
hemi="{hemi,Lflip|R}"
),
group:
"subj"
container:
config["singularity"]["autotop"]
threads: 8
shell:
"greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {input.template_seg} {output.inject_seg} -r {input.warp} {input.matrix}"
"greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {input.template_seg} {output.inject_seg} -r {input.warp} {input.matrix} &> {log}"


rule inject_init_laplace_coords:
Expand Down Expand Up @@ -316,13 +322,23 @@ rule inject_init_laplace_coords:
space="corobl",
hemi="{hemi}"
),
log:
bids(
root="logs",
**config["subj_wildcards"],
dir="{dir}",
label="{autotop}",
suffix="injectcoords.txt",
desc="init",
hemi="{hemi}"
),
group:
"subj"
container:
config["singularity"]["autotop"]
threads: 8
shell:
"greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {input.coords} {output.init_coords} -r {input.warp} {input.matrix}"
"greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {input.coords} {output.init_coords} -r {input.warp} {input.matrix} &> {log}"


rule reinsert_subject_labels:
Expand Down
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