Use synthsr conda package

autoafids/workflow/envs/synthsr.yaml

@@ -1,10 +1,6 @@
 ---
 name: synthsr
-channels: [anaconda, conda-forge, defaults]
+channels: [khanlab, anaconda, conda-forge, defaults]
 dependencies:
   - python=3.8
-  - tensorflow=2.2.0
-  - keras=2.3.1
-  - nibabel
-  - matplotlib
-  - numpy<1.20
+  - synthsr

autoafids/workflow/scripts/run_synthsr.py

@@ -3,46 +3,22 @@
 import subprocess
 
 
-# clone SynthSR repo
-def clone_repo(download_dir, log_file):
-    repo = "https://github.com/mackenziesnyder/SynthSR"
-    branch = "mackenzie/scaled-down-repo"
-
-    repo_dir = os.path.join(download_dir, "SynthSR")
-    if os.path.exists(repo_dir):
-        logging.info(
-            f"SynthSR repository already exists at {repo_dir}. Skipping clone."
-        )
-        return repo_dir
-
-    with open(log_file, "a") as log:
-        try:
-            subprocess.run(
-                ["git", "clone", "--branch", branch, repo, repo_dir],
-                check=True,
-                stdout=log,
-                stderr=log
-            )
-        except subprocess.CalledProcessError as e:
-            logging.error(f"Error cloning SynthSR repo: {e}")
-            raise
-
-    return repo_dir
-
 # run SynthSR
 def run_program(
-        repo_dir,
         input_img,
         output_img,
         modality,
         log_file
     ):
-    predict_script = os.path.join(
-        repo_dir,
-        "scripts",
-        "predict_command_line.py"
-    )
-    cmd = ["python", predict_script, input_img, output_img, "--cpu"]
+
+    cmd = [
+        "python",
+        "-m",
+        "SynthSR.scripts.predict_command_line",
+        input_img,
+        output_img,
+        "--cpu"
+    ]
 
     if modality == "ct":
         cmd.append["--ct"]
@@ -66,10 +42,8 @@ def run_program(
 
 log_file=snakemake.log[0]
 download_dir=snakemake.params["download_dir"]
-repo_dir = clone_repo(download_dir, log_file)
 
 run_program(
-    repo_dir=repo_dir,
     input_img=snakemake.input["im"],
     output_img=snakemake.output["SynthSR"],
     modality=snakemake.params["modality"],