specify extension of input files

rosalindfranklininstitute · Feb 22, 2023 · 8738ec4 · 8738ec4
1 parent 2bd5143
commit 8738ec4
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Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/src/Ot2Rec/aretomo.py b/src/Ot2Rec/aretomo.py
@@ -366,7 +366,7 @@ def update_yaml(args):
     if args["aretomo_mode"] != 1:  # for workflows with alignment
         # Set InMrc
         st_file_list = _find_files_with_ext(
-            ".st",
+            args["input_ext"],
             rootname,
             suffix,
             str(args["input_mrc_folder"])
@@ -405,7 +405,12 @@ def update_yaml(args):
         aretomo_params.params["AreTomo_setup"]["tilt_angles"] = tlt_file_list
 
         # Set process list
-        ts_list = _get_process_list(st_file_list, rootname, suffix, ".st")
+        ts_list = _get_process_list(
+            st_file_list,
+            rootname,
+            suffix,
+            args["input_ext"]
+        )
         aretomo_params.params["System"]["process_list"] = ts_list
 
         # Set output mrc

diff --git a/src/Ot2Rec/magicgui.py b/src/Ot2Rec/magicgui.py
@@ -772,7 +772,7 @@ def get_args_imod_route(
         "max": 2,
         "step": 1,
     },
-    rot_angle={"label": "Rotation angle of electron beam*, can be obtained from mdoc",
+    rot_angle={"label": "Rotation angle of electron beam, can be obtained from mdoc",
                "min": -180.0000,
                "max": 180.0000
     },
@@ -785,6 +785,10 @@ def get_args_imod_route(
         "label": "Folder containing input mrc's",
         "mode": "d",
     },
+    input_ext={
+        "label": "Extension of input mrc files",
+        "tooltip": ".st or .mrc usually"
+    },
     output_path={
         "label": "Path to output folder",
         "mode": "d",
@@ -826,6 +830,7 @@ def get_args_aretomo(
         rootname="",
         suffix="",
         input_mrc_folder=Path("./aretomo"),
+        input_ext=".st",
         output_path=Path("./aretomo"),
         tilt_angles="",
         volz=-1,