0.4.0 beamshiftnaming

conda-build/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: ot2rec
-  version: 0.3.2
+  version: 0.4.0_post1
 
 source:
   path: ..

construct.yaml

@@ -1,10 +1,10 @@
 name: Ot2Rec
-version: 0.3.2
+version: 0.4.0_post1
 company: Rosalind Franklin Institute
 channels:
   - https://conda.anaconda.org/conda-forge
   - file:///usr/share/miniconda3/conda-bld/
 specs:
   - python 3.9.*
-  - Ot2Rec 0.3.2
+  - Ot2Rec 0.4.0_post1
   - conda

setup.py

@@ -17,7 +17,7 @@
 
 
 setup(
-    version="0.3.2",
+    version="0.4.0_post1",
     name="Ot2Rec",
     description="Ot2Rec",
     url="https://github.com/rosalindfranklininstitute/Ot2Rec",
@@ -70,7 +70,8 @@
             "o2r.deconv.run=Ot2Rec.rlf_deconv:run",
             "o2r.cleanup=Ot2Rec.main:cleanup",
             "o2r.runall.imod=Ot2Rec.main:run_all_imod",
-            "o2r.previewer=Ot2Rec.previewer:run_previewer",
+            "o2r.previewer=Ot2Rec.previewer:run_previewer_with_mgui",
+            "o2r.rename=Ot2Rec.utils.rename:rename_all_with_mgui",
         ]
     },
 )

src/Ot2Rec/__init__.py

@@ -1,31 +0,0 @@
-# Copyright 2021 Rosalind Franklin Institute
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
-# either express or implied. See the License for the specific
-# language governing permissions and limitations under the License.
-
-
-# Ot2Rec Imports
-from . import params
-from . import metadata
-from . import motioncorr
-from . import logger
-from . import ctffind
-from . import align
-from . import recon
-from . import main
-from . import previewer
-
-
-VERSION = "v1.0a"
-"""
-str : Ot2Rec version string.
-"""

src/Ot2Rec/align.py

@@ -27,7 +27,6 @@
 import yaml
 from beautifultable import BeautifulTable as bt
 
-from . import user_args as uaMod
 from . import mgui_imod_align as mgMod
 from . import metadata as mdMod
 from . import params as prmMod
@@ -91,7 +90,7 @@ def _get_internal_metadata(self):
             columns=["ts", "stack_output", "align_output"]
         )
         for curr_ts in self.params["System"]["process_list"]:
-            subfolder_name = f"{self.rootname}_{curr_ts}{self.suffix}"
+            subfolder_name = f"{self.rootname}_{curr_ts:03}{self.suffix}"
             _to_append = pd.DataFrame(
                 {
                     "ts": [curr_ts],
@@ -167,8 +166,11 @@ def _check_aligned_images(self):
 
         self._merged = self._align_images.merge(_ignored, how="left", indicator=True)
         self._align_images = self._align_images[self._merged["_merge"] == "left_only"]
-        self._process_list = (
-            self._align_images["ts"].sort_values(ascending=True).unique().tolist()
+        # self._process_list = (
+        #     self._align_images["ts"].sort_values(ascending=True).unique().tolist()
+        # )
+        self._process_list = sorted(
+            list(self._align_images["ts"].unique().astype("int"))
         )
 
     """
@@ -201,7 +203,7 @@ def create_stack_folders(self, single_folder=False):
         else:
             for curr_ts in self._process_list:
                 subfolder_path = (
-                    f"{self.basis_folder}/{self.rootname}_{curr_ts}{self.suffix}"
+                    f"{self.basis_folder}/{self.rootname}_{curr_ts:03}{self.suffix}"
                 )
                 os.makedirs(subfolder_path, exist_ok=True)
                 self._path_dict[curr_ts] = subfolder_path
@@ -239,7 +241,7 @@ def create_rawtlt(self):
             # Define path where the new rawtlt file should go
             rawtlt_file = (
                 f"{self._path_dict[curr_ts]}/{self.params['System']['output_rootname']}_"
-                f"{curr_ts}{self.params['System']['output_suffix']}.rawtlt"
+                f"{curr_ts:03}{self.params['System']['output_suffix']}.rawtlt"
             )
 
             # Sort the filtered metadata
@@ -316,7 +318,9 @@ def create_stack(self):
             self.export_metadata()
 
         if error_count == 0:
-            self.logObj.logger.info("All Ot2Rec-align (IMOD): newstack jobs successfully finished.")
+            self.logObj.logger.info(
+                "All Ot2Rec-align (IMOD): newstack jobs successfully finished."
+            )
         else:
             self.logObj.logger.warning(
                 "All Ot2Rec-align (IMOD): newstack jobs finished. {error_count} of {len(tqdm_iter)} jobs failed.",
@@ -602,8 +606,7 @@ def update_yaml(args, logger=None):
         args (Namespace): Namespace generated with user inputs
     """
     if logger is None:
-        log_align = logMod.Logger(name="imod_align",
-                                  log_path="")
+        log_align = logMod.Logger(name="imod_align", log_path="")
     else:
         log_align = logger
 
@@ -616,7 +619,7 @@ def update_yaml(args, logger=None):
             "Error in Ot2Rec.align.update_yaml: alignment config file not found."
         )
     if not os.path.isfile(mc2_yaml_name):
-        log_align.logger.error(message="MotionCor2 config file not found.")
+        log_align.logger.error("MotionCor2 config file not found.")
         raise IOError(
             "Error in Ot2Rec.align.update__yaml: motioncorr config file not found."
         )
@@ -659,7 +662,9 @@ def update_yaml(args, logger=None):
         project_name=args.project_name, filename=mc2_yaml_name
     )
 
-    align_params.params["System"]["process_list"] = unique_ts_numbers
+    align_params.params["System"]["process_list"] = [
+        int(ts) for ts in unique_ts_numbers
+    ]
     align_params.params["BatchRunTomo"]["setup"]["pixel_size"] = (
         mc2_params.params["MC2"]["desired_pixel_size"] * 0.1
     )

src/Ot2Rec/aretomo.py

@@ -28,7 +28,6 @@
 from . import align
 from . import logger as logMod
 from . import params as prmMod
-from . import user_args as uaMod
 from . import mgui_imod_align as imod_newstack_MGUI
 from . import mgui_aretomo as mgMod
 
@@ -97,17 +96,18 @@ def _get_internal_metadata(self):
         )
         for i, curr_ts in enumerate(self.params["System"]["process_list"]):
             subfolder = (
-                f"{self.basis_folder}/" f"{self.rootname}_{curr_ts}{self.suffix}"
+                f"{self.basis_folder}/" f"{self.rootname}_{curr_ts:03}{self.suffix}"
             )
             os.makedirs(subfolder, exist_ok=True)
             # self._path_dict[curr_ts] = subfolder
             if "aretomo_output_dir" not in list(self.md_out.keys()):
                 self.md_out["aretomo_output_dir"] = {}
                 self.md_out["aretomo_align_stats"] = {}
             self.md_out["aretomo_output_dir"][curr_ts] = subfolder
-            input_img_name = os.path.splitext(
-                os.path.basename(self.params["AreTomo_setup"]["input_mrc"][i])
-            )[0]
+            input_img_name = os.path.basename(
+                self.params["AreTomo_setup"]["input_mrc"][i]
+            )
+
             self.md_out["aretomo_align_stats"][
                 curr_ts
             ] = f"{subfolder}/{input_img_name}.aln"
@@ -261,7 +261,9 @@ def export_metadata(self):
             for ts in list(self.sta.keys()):
                 sta_ts_folder = f"{self.sta_folder}/{self.sta[ts].split(os.sep)[-2]}"
                 if os.path.exists(sta_ts_folder):
-                    self.logObj.logger.warning(f"STA folder {sta_ts_folder} not empty, overwriting.")
+                    self.logObj.logger.warning(
+                        f"STA folder {sta_ts_folder} not empty, overwriting."
+                    )
                     shutil.rmtree(sta_ts_folder)
                 shutil.move(
                     src=self.sta[ts],
@@ -303,15 +305,18 @@ def _update_volz(args, aretomo_params):
 def _create_stacks_with_imod(args):
     # Uses align to create the InMrc and AngFile in correct form
     try:
-        args_in_align = imod_newstack_MGUI.get_args_align
-        args_in_align.project_name.value = args["project_name"]
-        args_in_align.rot_angle.value = args["rot_angle"]
-        args_in_align.output_folder.value = args["output_path"]
-        align.create_yaml(args_in=args_in_align)
-        align.run(newstack=True, do_align=False, args_pass=[args["project_name"]])
+        args_in_align = asObject(imod_newstack_MGUI.get_args_align(return_only=True))
+        args_in_align.project_name = args["project_name"]
+        args_in_align.rot_angle = args["rot_angle"]
+        args_in_align.output_folder = args["output_path"]
+        args_in_align.pixel_size = args["pixel_size"]
+        args_in_align.file_ext = "st"
+        prmMod.new_align_yaml(args_in_align)
+        align.update_yaml(args_in_align, None)
+        align.run(newstack=True, do_align=False, args_in=args_in_align, exclusive=False)
         print("Created stacks for input to AreTomo")
     except:
-        warnings.warn("Stacks could not be created, IMOD might not be loaded")
+        raise ImportError("Stacks could not be created, IMOD might not be loaded")
 
 
 def _find_files_with_ext(ext, rootname, suffix, directory):
@@ -337,13 +342,14 @@ def _get_yaml_filename(aretomo_mode, project_name):
 def _get_process_list(file_list, rootname, suffix, ext):
     ts_list = []
     for st in file_list:
-        st_bn = os.path.basename(st)
-        if suffix != "":
-            ts_list.append(
-                st_bn.split(f"{rootname}_")[1].split(f"_{suffix}{ext}")[0][:-1]
-            )
-        else:
-            ts_list.append(st_bn.split(f"{rootname}_")[1].split(ext)[0][:-1])
+        st_bn = os.path.splitext(os.path.basename(st))[0]
+        # if suffix != "":
+        #     ts_list.append(
+        #         # int(st_bn.split(f"{rootname}_")[1].split(f"_{suffix}{ext}")[0][:-1])
+        #     )
+        # else:
+        #     ts_list.append(int(st_bn.split(f"{rootname}_")[1].split(ext)[0][:-1]))
+        ts_list.append(int(st_bn.split("_")[-1]))
     return ts_list
 
 
@@ -426,8 +432,8 @@ def update_yaml(args):
         out_file_list = [
             (
                 f"{aretomo_params.params['System']['output_path']}/"
-                f"{rootname}_{curr_ts}{suffix}/"
-                f"{rootname}_{curr_ts}{suffix}{ext}"
+                f"{rootname}_{curr_ts:03}{suffix}/"
+                f"{rootname}_{curr_ts:03}{suffix}{ext}"
             )
             for curr_ts in ts_list
         ]

src/Ot2Rec/ctffind.py

@@ -24,7 +24,6 @@
 import pandas as pd
 from icecream import ic
 
-from . import user_args as uaMod
 from . import mgui_ctffind as mgMod
 from . import metadata as mdMod
 from . import logger as logMod

src/Ot2Rec/ctfsim.py

@@ -31,7 +31,6 @@
 
 from icecream import ic
 
-from . import user_args as uaMod
 from . import magicgui as mgMod
 from . import metadata as mdMod
 from . import logger as logMod