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delete conda env from rules and default configfile from the workflows #56

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delete conda env from rules and default configfile from the workflows #56

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4 changes: 0 additions & 4 deletions workflows/apply_transform.smk
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
import json
import re

configfile: "examples/register_config_test_rigid_apply_transform.yaml"

moving_images = config["moving_images"]
moving_paths = [item["input_path"] for item in moving_images]
moving_keys = [item["input_key"] for item in moving_images]
Expand Down Expand Up @@ -57,7 +55,6 @@ rule apply_transform_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 \
Expand Down Expand Up @@ -93,7 +90,6 @@ rule apply_transform_n5:
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 \
Expand Down
11 changes: 0 additions & 11 deletions workflows/registration.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ from pathlib import Path
root_dir = f"{Path(workflow.basedir).resolve().parent}/"
print(f"working directory: {root_dir}")
workdir: root_dir
configfile: "examples/register_config_test_rigid.yaml"

print(config["fixed_image"])
print(config["moving_image"])
Expand Down Expand Up @@ -90,7 +89,6 @@ rule input_to_n5:
params:
output_key = raw_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"rm -r {{output.fixed_image_n5}};"
f"rm -r {{output.moving_image_n5}};"
Expand All @@ -116,7 +114,6 @@ rule SVD_prealignment:
output_key = prealignment_n5_key,
axis_orientation = config["prealignment"]["axis_orientation"]
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/prealignment.py --fixed_path {{input.fixed_image_n5}} --fixed_key {{params.input_key}} --fixed_spacing {{fixed_spacing}} --moving_path {{input.moving_image_n5}} --moving_key {{params.input_key}} --moving_spacing {{moving_spacing}} --output_dir {log_dir}/{{params.output_key}} --output_key {{params.output_key}} --output_transform_path {{output.output_transform}} --axis_orientation {{params.axis_orientation}};"

Expand All @@ -137,7 +134,6 @@ rule rigid_alignment:
input_key = prealignment_n5_key,
output_key = rigid_alignment_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/rigid_alignment_elastix.py --fixed_path {{input.fixed_image_n5}} --fixed_key {{params.input_key}} --moving_path {{input.moving_image_n5}} --moving_key {{params.input_key}} --output_dir {log_dir}/{{params.output_key}} --output_key {{params.output_key}};"

Expand All @@ -157,7 +153,6 @@ rule create_mobie_project:
params:
input_key = raw_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/mobie_export.py --input_path {{input.fixed_image_n5}} --input_key {{params.input_key}} --input_type {fixed_type} {'--semantic_seg' if semantic_seg else ''} --dataset_name {dataset_name} --output_dir {log_dir};"
f"touch {{output.fixed_check}};"
Expand Down Expand Up @@ -186,7 +181,6 @@ rule add_prealignment_to_mobie:
params:
input_key = prealignment_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/mobie_export.py --input_path {{input.fixed_image_n5}} --input_key {{params.input_key}} --input_type {fixed_type} {'--semantic_seg' if semantic_seg else ''} --dataset_name {dataset_name} --output_dir {log_dir};"
f"touch {{output.fixed_check}};"
Expand All @@ -212,7 +206,6 @@ rule add_rigid_alignment_to_mobie:
params:
input_key = rigid_alignment_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/mobie_export.py --input_path {{input.moving_image_n5}} --input_key {{params.input_key}} --input_type {moving_type} {'--semantic_seg' if semantic_seg else ''} --dataset_name {dataset_name} --output_dir {log_dir};"
f"touch {{output.moving_check}};"
Expand All @@ -234,7 +227,6 @@ rule cpd_nonrigid_registration:
fixed_key = prealignment_n5_key,
moving_key = rigid_alignment_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/cpd_nonrigid_registration.py --moving_path {{input.moving_image_n5}} --moving_key {{params.moving_key}} --fixed_path {{input.fixed_image_n5}} --fixed_key {{params.fixed_key}} -o {{params.log_dir}} --w {w} --beta {beta} --lmd {lmd} --maxiter {maxiter};"

Expand All @@ -248,7 +240,6 @@ rule ilp_matching:
params:
log_dir = f"{log_dir}/match_pointclouds"
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/match_pointclouds.py --fixed_pcd {{input.fixed_pcd}} --moving_pcd {{input.moving_pcd}} -o {{params.log_dir}} --min_neighbours {min_neighbours} --max_dist {max_dist};"

Expand All @@ -273,7 +264,6 @@ rule elastix_deformable_pointset:
prealigned_output_key = pointset_alignment_n5_key,
log_dir = f"{log_dir}/elastix_deformable_pointset_registration"
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/elastix_deformable_pointset_registration.py --fixed_path {{input.fixed_image_n5}} --fixed_key {{params.input_key}} --moving_path {{input.moving_image_n5}} --moving_key {{params.input_key}} --output_dir {{params.log_dir}} --output_key {{params.output_key}} --match_path {{input.match_path}} --prealigned_output_key {{params.prealigned_output_key}} --prealignment_transform {{input.prealignment_transform}};"

Expand All @@ -288,7 +278,6 @@ rule add_elastix_deformable_pointset_to_mobie:
params:
input_key = pointset_alignment_input_space_n5_key
log: f"{log_dir}/matchmaker.log"
conda: "matchmaker_env"
shell:
f"python matchmaker/mobie_export.py --input_path {{input.moving_image_n5}} --input_key {{params.input_key}} --input_type {moving_type} {'--semantic_seg' if semantic_seg else ''} --dataset_name {dataset_name} --output_dir {log_dir};"
f"touch {{output.moving_check}};"
Expand Down