Performance updates

spimquant/config/snakebids.yml

@@ -155,7 +155,6 @@ parse_args:
     help: "Method to use for microscopy segmentation (e.g. plaques, protein deposits, cells) applied to 'stains_for_seg' channels, and used to calculate field fractions. "
     default: 
       - otsu+k3i2
-      - th900
     nargs: '+'
 
   --seg_hist_range:
@@ -189,7 +188,7 @@ parse_args:
     choices:
       - threads
       - distributed
-    default: threads
+    default: distributed
 
   --sloppy:
     help: "Use low-quality parameters for speed (USE FOR TESTING ONLY)"

spimquant/workflow/Snakefile

@@ -271,6 +271,20 @@ rule all_vessels:
         ),
 
 
+#        inputs["spim"].expand(
+#            bids(
+#                root=root,
+#                datatype="micr",
+#                stain="{stain}",
+#                desc="{desc}",
+#                suffix="mask.ozx",
+#                **inputs["spim"].wildcards,
+#            ),
+#            desc=config["vessel_seg_method"],
+#            stain=stains_for_vessels,
+#        )
+
+
 rule all_segment:
     input:
         inputs["spim"].expand(
@@ -676,7 +690,6 @@ rule all_participant:
         rules.all_register.input,
         rules.all_vessels.input if do_vessels else [],
         rules.all_segment.input if do_seg else [],
-        rules.all_spim_patches.input if do_seg else [],
         rules.all_mri_reg.input if config["register_to_mri"] else [],
         rules.all_segment_coloc.input if do_coloc else [],
         rules.all_segment_maskcoloc.input if do_maskcoloc else [],

spimquant/workflow/rules/groupstats.smk

@@ -46,7 +46,7 @@ rule perform_group_stats:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
+        mem_mb=1500,
         runtime=10,
     script:
         "../scripts/perform_group_stats.py"
@@ -89,7 +89,7 @@ rule create_stats_heatmap:
     threads: 1
     resources:
         mem_mb=8000,
-        runtime=5,
+        runtime=15,
     script:
         "../scripts/create_stats_heatmap.py"
 
@@ -131,7 +131,7 @@ rule map_groupstats_to_template_nii:
     threads: 8
     resources:
         mem_mb=16000,
-        runtime=5,
+        runtime=15,
     script:
         "../scripts/map_tsv_dseg_to_nii.py"
 
@@ -167,7 +167,7 @@ rule concat_subj_parquet:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
+        mem_mb=1500,
         runtime=10,
     script:
         "../scripts/concat_subj_parquet.py"
@@ -196,12 +196,10 @@ rule group_counts_per_voxel:
             desc="{desc}",
             suffix="{stain}+count.nii.gz",
         ),
-    group:
-        "subj"
     threads: 16
     resources:
-        mem_mb=15000,
-        runtime=10,
+        mem_mb=200000,
+        runtime=30,
     script:
         "../scripts/counts_per_voxel_template.py"
 
@@ -229,8 +227,6 @@ rule group_coloc_counts_per_voxel:
             desc="{desc}",
             suffix="coloccount.nii.gz",
         ),
-    group:
-        "subj"
     threads: 16
     resources:
         mem_mb=15000,
@@ -275,7 +271,7 @@ rule concat_subj_parquet_contrast:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
+        mem_mb=1500,
         runtime=10,
     script:
         "../scripts/concat_subj_parquet_contrast.py"
@@ -306,12 +302,10 @@ rule group_counts_per_voxel_contrast:
             contrast="{contrast_column}+{contrast_value}",
             suffix="{stain}+count.nii.gz",
         ),
-    group:
-        "subj"
     threads: 16
     resources:
-        mem_mb=15000,
-        runtime=10,
+        mem_mb=200000,
+        runtime=30,
     script:
         "../scripts/counts_per_voxel_template.py"
 
@@ -341,8 +335,6 @@ rule group_coloc_counts_per_voxel_contrast:
             contrast="{contrast_column}+{contrast_value}",
             suffix="coloccount.nii.gz",
         ),
-    group:
-        "subj"
     threads: 16
     resources:
         mem_mb=15000,
@@ -395,7 +387,7 @@ rule concat_subj_segstats_contrast:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
+        mem_mb=1500,
         runtime=10,
     script:
         "../scripts/concat_subj_segstats_contrast.py"
@@ -441,6 +433,6 @@ rule map_groupavg_segstats_to_template_nii:
     threads: 8
     resources:
         mem_mb=16000,
-        runtime=5,
+        runtime=15,
     script:
         "../scripts/map_tsv_dseg_to_nii.py"

spimquant/workflow/rules/import.smk

@@ -42,12 +42,10 @@ rule get_downsampled_nii:
             suffix="SPIM.nii.gz",
             **inputs["spim"].wildcards,
         ),
-    group:
-        "subj"
     threads: 32
     resources:
         mem_mb=16000,
-        runtime=5,
+        runtime=15,
     script:
         "../scripts/ome_zarr_to_nii.py"
 
@@ -77,8 +75,8 @@ rule import_template_anat:
         anat=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     log:
         bids_tpl(
             root="logs",
@@ -109,8 +107,8 @@ rule import_template_spim:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     log:
         bids_tpl(
             root="logs",
@@ -133,8 +131,8 @@ rule import_mask:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     log:
         bids_tpl(
             root="logs",
@@ -153,8 +151,8 @@ rule generic_lut_bids_to_itksnap:
         lut="{prefix}_dseg.itksnap.txt",
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     script:
         "../scripts/lut_bids_to_itksnap.py"
 
@@ -182,8 +180,8 @@ rule import_dseg:
         ),
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     script:
         "../scripts/copy_nii.py"
 
@@ -201,8 +199,8 @@ rule import_lut_tsv:
         tsv=bids_tpl(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     shell:
         "cp {input} {output}"
 
@@ -214,7 +212,7 @@ rule import_DSURQE_tsv:
         tsv=bids_tpl(root=root, template="DSURQE", seg="all", suffix="dseg.tsv"),
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=1500,
+        runtime=15,
     script:
         "../scripts/import_DSURQE_dseg_tsv.py"

spimquant/workflow/rules/masking.smk

@@ -49,7 +49,7 @@ rule pre_atropos:
                 desc="preAtropos",
                 suffix="SPIM.nii.gz",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
         mask=temp(
             bids(
@@ -60,14 +60,12 @@ rule pre_atropos:
                 desc="preAtropos",
                 suffix="mask.nii",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
-    group:
-        "subj"
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=3000,
+        runtime=15,
     conda:
         "../envs/c3d.yaml"
     shell:
@@ -98,7 +96,7 @@ rule atropos_seg:
                 k="{k}",
                 suffix="dseg.nii",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
         posteriors_dir=temp(
             directory(
@@ -112,18 +110,16 @@ rule atropos_seg:
                     suffix="posteriors",
                     **inputs["spim"].wildcards,
                 )
-            )
+            ),
         ),
-    group:
-        "subj"
     conda:
         "../envs/ants.yaml"
     shadow:
         "minimal"
-    threads: 1
+    threads: 16
     resources:
-        mem_mb=8000,
-        runtime=15,
+        mem_mb=32000,
+        runtime=45,
     shell:
         "mkdir -p {output.posteriors_dir} && "
         "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
@@ -155,14 +151,12 @@ rule post_atropos:
                 k="{k}",
                 suffix="dseg.nii",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
-    group:
-        "subj"
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=3000,
+        runtime=15,
     conda:
         "../envs/c3d.yaml"
     shell:
@@ -199,7 +193,7 @@ rule init_affine_reg:
                 desc="initaffine",
                 suffix="xfm.txt",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
         warped=temp(
             bids(
@@ -209,10 +203,8 @@ rule init_affine_reg:
                 desc="initaffinewarped",
                 suffix="SPIM.nii.gz",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
-    group:
-        "subj"
     log:
         bids(
             root="logs",
@@ -224,7 +216,7 @@ rule init_affine_reg:
     threads: 32
     resources:
         mem_mb=16000,
-        runtime=5,
+        runtime=15,
     shell:
         "greedy -threads {threads} -d 3 -i {input.template} {input.subject} "
         " -a -dof 12 -ia-image-centers -m NMI -o {output.xfm_ras} -n {params.iters} && "
@@ -254,14 +246,12 @@ rule affine_transform_template_mask_to_subject:
                 from_="{template}",
                 suffix="mask.nii.gz",
                 **inputs["spim"].wildcards,
-            )
+            ),
         ),
-    group:
-        "subj"
     threads: 32
     resources:
         mem_mb=16000,
-        runtime=5,
+        runtime=15,
     shell:
         " greedy -threads {threads} -d 3 -rf {input.ref} "
         " -ri NN"
@@ -307,12 +297,10 @@ rule create_mask_from_gmm_and_prior:
             suffix="mask.nii.gz",
             **inputs["spim"].wildcards,
         ),
-    group:
-        "subj"
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=4000,
+        runtime=15,
     script:
         "../scripts/create_mask_from_gmm_and_prior.py"
 
@@ -341,12 +329,10 @@ rule create_mask_from_gmm:
             suffix="mask.nii.gz",
             **inputs["spim"].wildcards,
         ),
-    group:
-        "subj"
     threads: 1
     resources:
-        mem_mb=16000,
-        runtime=5,
+        mem_mb=4000,
+        runtime=15,
     conda:
         "../envs/c3d.yaml"
     shell: