handle for read-only template files

FCP-INDI · Sep 18, 2024 · 4d2f933 · 4d2f933
1 parent 400e36a
commit 4d2f933
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Showing 2 changed files with 96 additions and 69 deletions.
diff --git a/CPAC/pipeline/engine.py b/CPAC/pipeline/engine.py
@@ -2503,27 +2503,31 @@ def ingress_pipeconfig_paths(wf, cfg, rpool, unique_id, creds_path=None):
             output = "outputspec.data"
             node_name = f"{key}_config_ingress"
 
-        # check if the output is in desired orientation, if not reorient it
-        check_orient = pe.Node(
-            Function(
-                input_names=["input_file", "desired_orientation", "reorient"],
-                output_names=["output_file"],
-                function=check_orientation,
-            ),
-            name=f"check_orient_{key}",
-        )
-        wf.connect(node, output, check_orient, "input_file")
-        check_orient.inputs.desired_orientation = desired_orientation
-        check_orient.inputs.reorient = True
-
-        rpool.set_data(
-            key,
-            check_orient,
-            "output_file",
-            json_info,
-            "",
-            f"check_orient-{node_name}-{key}",
-        )
+        if val.endswith(".nii.gz"):
+            # check if the output is in desired orientation, if not reorient it
+            check_orient = pe.Node(
+                Function(
+                    input_names=["input_file", "desired_orientation", "reorient"],
+                    output_names=["output_file"],
+                    function=check_orientation,
+                    imports=["from CPAC.pipeline.utils import reorient_image"],
+                ),
+                name=f"check_orient_{key}",
+            )
+            wf.connect(node, output, check_orient, "input_file")
+            check_orient.inputs.desired_orientation = desired_orientation
+            check_orient.inputs.reorient = True
+
+            rpool.set_data(
+                key,
+                check_orient,
+                "output_file",
+                json_info,
+                "",
+                f"check_orient-{node_name}-{key}",
+            )
+        else:
+            rpool.set_data(key, node, output, json_info, "", node_name)
     # templates, resampling from config
     """
     template_keys = [

diff --git a/CPAC/pipeline/utils.py b/CPAC/pipeline/utils.py
@@ -25,80 +25,103 @@
 MOVEMENT_FILTER_KEYS = motion_estimate_filter.outputs
 
 
-def check_orientation(input_file, desired_orientation, reorient=False):
-    """Find the orientation of the input file and reorient it if necessary.
+def reorient_image(input_file, orientation):
+    """Reorient the input image to the desired orientation. Replaces the original input_file with the reoriented image.
 
     Parameters
     ----------
     input_file : str
-        Input file path
-    desired_orientation : str
-        Desired orientation of the input file
-    reorient : bool
-        Reorient the input file to the desired orientation
+        Input image file path
+    orientation : str
+        Desired orientation of the input image
 
     Returns
     -------
-    orientation : str
-        Orientation of the input file
+    output_file : str
+        Reoriented image file path
     """
+    import os
+    import shutil
     import subprocess
 
-    cmd_3dinfo = ["3dinfo", "-orient", input_file]
-
-    orientation = (
-        subprocess.run(cmd_3dinfo, capture_output=True, text=True, check=False)
-        .stdout.strip()
-        .upper()
+    output_file = os.path.join(
+        os.getcwd(),
+        f"reoriented_{os.path.basename(input_file)}",
     )
-    if orientation != desired_orientation and reorient:
-        output_file = reorient_image(input_file, desired_orientation)
-    else:
-        output_file = input_file
+    # if output file exist delete it
+    if os.path.exists(output_file):
+        os.remove(output_file)
+
+    # make a copy of the input file as temp file so that the original file is not modified
+    temp_file = os.path.join(
+        os.getcwd(),
+        f"temp_{os.path.basename(input_file)}",
+    )
+    shutil.copy(input_file, temp_file)
+
+    cmd_3drefit = ["3drefit", "-deoblique", temp_file]
+    cmd_3dresample = [
+        "3dresample",
+        "-orient",
+        orientation,
+        "-prefix",
+        output_file,
+        "-inset",
+        temp_file,
+    ]
+    subprocess.run(cmd_3drefit, check=True)
+    subprocess.run(cmd_3dresample, check=True)
+
+    # remove the temporary file
+    os.remove(temp_file)
+
     return output_file
 
 
-def reorient_image(input_file, orientation):
-    """Reorient the input image to the desired orientation. Replaces the original input_file with the reoriented image.
+def check_orientation(input_file, desired_orientation, reorient=True):
+    """Find the orientation of the input file and reorient it if necessary. Does not modify the original input file.
 
     Parameters
     ----------
     input_file : str
-        Input image file path
-    orientation : str
-        Desired orientation of the input image
+        Input file path
+    desired_orientation : str
+        Desired orientation of the input file
+    reorient : bool
+        Reorient the input file to the desired orientation
 
     Returns
     -------
     output_file : str
         Reoriented image file path
     """
-    try:
-        import os
-        import subprocess
+    import subprocess
 
-        output_file = os.path.join(
-            os.path.dirname(input_file),
-            f"reoriented_{os.path.basename(input_file)}",
-        )
-        cmd_3drefit = ["3drefit", "-deoblique", input_file]
-        cmd_3dresample = [
-            "3dresample",
-            "-orient",
-            orientation,
-            "-prefix",
-            output_file,
-            "-inset",
-            input_file,
-        ]
+    cmd_3dinfo = ["3dinfo", "-orient", input_file]
 
-        IFLOGGER.info(f"""+++\nReorienting : {input_file}\nto : {orientation}\n+++""")
-        subprocess.run(cmd_3drefit, check=True)
-        subprocess.run(cmd_3dresample, check=True)
-        return output_file
-    except Exception as e:
-        IFLOGGER.error(f"Reorienting failed for {input_file} with error: {e}")
-        return input_file
+    orientation = (
+        subprocess.run(cmd_3dinfo, capture_output=True, text=True, check=False)
+        .stdout.strip()
+        .upper()
+    )
+    if orientation != desired_orientation and reorient:
+        IFLOGGER.info(
+            f"+++ Reorienting {input_file} from {orientation} to {desired_orientation} +++"
+        )
+        try:
+            output_file = reorient_image(input_file, desired_orientation)
+        except Exception as e:
+            IFLOGGER.error(
+                f"Error in reorienting the image: {input_file}.\nCould not reorient the image to {desired_orientation}"
+            )
+            IFLOGGER.error(f"Error: {e}")
+            output_file = input_file  # return the original file ?
+    else:
+        IFLOGGER.info(
+            f"+++ Orientation of {input_file} is already {desired_orientation} +++"
+        )
+        output_file = input_file
+    return output_file
 
 
 def name_fork(resource_idx, cfg, json_info, out_dct):