Feature/czi stereotaxy

.readthedocs.yaml

@@ -15,7 +15,7 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF
 formats: [pdf]
 build:
-  os: ubuntu-20.04
+  os: "ubuntu-22.04"
   tools:
     python: '3.11'
 python:

autoafids/config/snakebids.yml

@@ -235,8 +235,9 @@ resource_urls:
 
 #Stereotaxy models 
 STN: 'resources/stereotaxy/STN.pkl'
-cZI: 'resources/stereotaxy/STN.pkl' #change to czi model but dummy here for testing
+cZI: 'resources/stereotaxy/cZI.pkl'
 template_fcsv: 'resources/stereotaxy/target_template.fcsv'
+cZI_template_fcsv: 'resources/stereotaxy/cZI_target_template.fcsv'
 
 plugins.validator.skip: False
 root: results

autoafids/resources/stereotaxy/cZI_target_template.fcsv

@@ -0,0 +1,5 @@
+# Markups fiducial file version = 4.11
+# CoordinateSystem = RAS
+# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
+1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,1,Predicted Right cZI ,vtkMRMLScalarVolumeNode1
+2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,2,Predicted Left cZI,vtkMRMLScalarVolumeNode1

autoafids/workflow/rules/stereotaxy.smk

@@ -1,15 +1,20 @@
 stereotaxy_target = config["stereotaxy"]
 
 
+def which_input(wildcards):
+    desc_val = "afidscnn-nnlm" if config.get("detect_mode") == "nnlm" else "afidscnn"
+    return bids(
+        root=root,
+        datatype="afids-cnn",
+        desc=desc_val,
+        suffix="afids.fcsv",
+        **inputs[config["modality"]].wildcards,
+    )
+
+
 rule stereotaxy:
     input:
-        afidfcsv=bids(
-            root=root,
-            datatype="afids-cnn",
-            desc=_fcsv_desc,
-            suffix="afids.fcsv",
-            **inputs[config["modality"]].wildcards,
-        ),
+        afidfcsv=which_input,
     output:
         fcsv_native=bids(
             root=root,
@@ -35,7 +40,14 @@ rule stereotaxy:
     params:
         model=str(Path(workflow.basedir).parent / config[stereotaxy_target]),
         midpoint="PMJ",
-        target_fcsv=str(Path(workflow.basedir).parent / config["template_fcsv"]),
+        target_fcsv=str(
+            Path(workflow.basedir).parent
+            / (
+                config["cZI_template_fcsv"]
+                if stereotaxy_target == "cZI"
+                else config["template_fcsv"]
+            )
+        ),
     conda:
         "../envs/skimage.yaml"
     script: