renamed spim to SPIM (for BIDS compliance) (#14)

khanlab · Apr 2, 2024 · 71c3201 · 71c3201
1 parent e7ea754
commit 71c3201
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Showing 6 changed files with 20 additions and 20 deletions.
diff --git a/workflow/rules/atlasreg.smk b/workflow/rules/atlasreg.smk
@@ -56,7 +56,7 @@ rule affine_reg:
             desc=config["atlasreg"]["desc"],
             stain=config["atlasreg"]["stain"],
             level=config["atlasreg"]["level"],
-            suffix="spim.nii",
+            suffix="SPIM.nii",
         ),
     output:
         xfm_ras=bids(
@@ -79,7 +79,7 @@ rule affine_reg:
             acq="{acq}",
             space="{template}",
             desc="affinewarped",
-            suffix="spim.nii",
+            suffix="SPIM.nii",
         ),
     log:
         bids(
@@ -111,7 +111,7 @@ rule deform_reg:
             desc=config["atlasreg"]["desc"],
             stain=config["atlasreg"]["stain"],
             level=config["atlasreg"]["level"],
-            suffix="spim.nii",
+            suffix="SPIM.nii",
         ),
         xfm_ras=rules.affine_reg.output.xfm_ras,
     output:
@@ -133,7 +133,7 @@ rule deform_reg:
             acq="{acq}",
             space="{template}",
             desc="deformwarped",
-            suffix="spim.nii",
+            suffix="SPIM.nii",
         ),
     log:
         bids(
@@ -167,7 +167,7 @@ rule resample_labels_to_zarr:
             acq="{acq}",
             desc="{desc}",
             stain=config["atlasreg"]["stain"],
-            suffix="spim.ome.zarr.zip",
+            suffix="SPIM.ome.zarr.zip",
         ),
     output:
         zarr=temp(

diff --git a/workflow/rules/bigstitcher.smk b/workflow/rules/bigstitcher.smk
@@ -7,7 +7,7 @@ rule zarr_to_bdv:
             sample="{sample}",
             acq="{acq}",
             desc="{desc}",
-            suffix="spim.zarr",
+            suffix="SPIM.zarr",
         ),
         metadata_json=rules.raw_to_metadata.output.metadata_json,
     params:
@@ -208,7 +208,7 @@ rule fuse_dataset:
                     acq="{acq}",
                     desc="stitched{desc}",
                     stain="{stain}",
-                    suffix="spim.zarr",
+                    suffix="SPIM.zarr",
                 )
             )
         ),
@@ -280,7 +280,7 @@ rule fuse_dataset_spark:
                     acq="{acq}",
                     desc="sparkstitched{desc}",
                     stain="{stain}",
-                    suffix="spim.zarr",
+                    suffix="SPIM.zarr",
                 )
             )
         ),

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -13,7 +13,7 @@ def get_all_targets():
                     datatype="micr",
                     sample="{sample}",
                     acq="{acq}",
-                    suffix="spim.ome.zarr.zip",
+                    suffix="SPIM.ome.zarr.zip",
                 ),
                 subject=datasets.loc[i, "subject"],
                 sample=datasets.loc[i, "sample"],
@@ -30,7 +30,7 @@ def get_all_targets():
                     acq="{acq}",
                     res="{level}x",
                     stain="{stain}",
-                    suffix="spim.nii",
+                    suffix="SPIM.nii",
                 ),
                 subject=datasets.loc[i, "subject"],
                 sample=datasets.loc[i, "sample"],

diff --git a/workflow/rules/flatfield_corr.smk b/workflow/rules/flatfield_corr.smk
@@ -9,7 +9,7 @@ rule fit_basic_flatfield_corr:
             sample="{sample}",
             acq="{acq}",
             desc="raw",
-            suffix="spim.zarr",
+            suffix="SPIM.zarr",
         ),
     params:
         channel=lambda wildcards: get_stains(wildcards).index(wildcards.stain),
@@ -71,7 +71,7 @@ rule apply_basic_flatfield_corr:
             sample="{sample}",
             acq="{acq}",
             desc="raw",
-            suffix="spim.zarr",
+            suffix="SPIM.zarr",
         ),
         model_dirs=lambda wildcards: expand(
             rules.fit_basic_flatfield_corr.output.model_dir,
@@ -88,7 +88,7 @@ rule apply_basic_flatfield_corr:
                     sample="{sample}",
                     acq="{acq}",
                     desc="flatcorr",
-                    suffix="spim.zarr",
+                    suffix="SPIM.zarr",
                 )
             )
         ),

diff --git a/workflow/rules/import.smk b/workflow/rules/import.smk
@@ -14,7 +14,7 @@ rule extract_dataset:
                     sample="{sample}",
                     acq="{acq}",
                     desc="raw",
-                    suffix="spim",
+                    suffix="SPIM",
                 )
             )
         ),
@@ -49,7 +49,7 @@ rule raw_to_metadata:
             datatype="micr",
             sample="{sample}",
             acq="{acq}",
-            suffix="spim.metadata.json",
+            suffix="SPIM.metadata.json",
         ),
     benchmark:
         bids(
@@ -100,7 +100,7 @@ rule tif_to_zarr:
                     sample="{sample}",
                     acq="{acq}",
                     desc="raw",
-                    suffix="spim.zarr",
+                    suffix="SPIM.zarr",
                 )
             )
         ),

diff --git a/workflow/rules/ome_zarr.smk b/workflow/rules/ome_zarr.smk
@@ -9,7 +9,7 @@ rule zarr_to_ome_zarr:
                 acq="{acq}",
                 desc="{desc}",
                 stain="{stain}",
-                suffix="spim.zarr",
+                suffix="SPIM.zarr",
             ),
             stain=get_stains(wildcards),
             desc=config["ome_zarr"]["desc"],
@@ -31,7 +31,7 @@ rule zarr_to_ome_zarr:
                     datatype="micr",
                     sample="{sample}",
                     acq="{acq}",
-                    suffix="spim.ome.zarr",
+                    suffix="SPIM.ome.zarr",
                 )
             )
         ),
@@ -75,7 +75,7 @@ rule ome_zarr_to_nii:
             datatype="micr",
             sample="{sample}",
             acq="{acq}",
-            suffix="spim.ome.zarr.zip",
+            suffix="SPIM.ome.zarr.zip",
         ),
     params:
         channel_index=lambda wildcards: get_stains(wildcards).index(wildcards.stain),
@@ -88,7 +88,7 @@ rule ome_zarr_to_nii:
             acq="{acq}",
             res="{level}x",
             stain="{stain}",
-            suffix="spim.nii",
+            suffix="SPIM.nii",
         ),
     benchmark:
         bids(