0.4.0 Previewer

setup.py

@@ -81,6 +81,7 @@
             "o2r.cleanup=Ot2Rec.main:cleanup",
 
             "o2r.runall.imod=Ot2Rec.main:run_all_imod",
+            "o2r.previewer=Ot2Rec.main:run_all_aretomo",
         ]
     }
 )

src/Ot2Rec/align.py

@@ -28,7 +28,7 @@
 from beautifultable import BeautifulTable as bt
 
 from . import user_args as uaMod
-from . import magicgui as mgMod
+from . import mgui_imod_align as mgMod
 from . import metadata as mdMod
 from . import params as prmMod
 from . import logger as logMod
@@ -84,13 +84,14 @@ def _get_internal_metadata(self):
         while self.rootname.endswith('_'):
             self.rootname = self.rootname[:-1]
         self.suffix = self.params['System']['output_suffix']
+        self.output_ext = self.params['System']['output_ext']
 
         self._align_images = pd.DataFrame(columns=['ts', 'stack_output', 'align_output'])
         for curr_ts in self.params['System']['process_list']:
-            subfolder_name = f'{self.rootname}_{curr_ts:04}{self.suffix}'
+            subfolder_name = f'{self.rootname}_{curr_ts}{self.suffix}'
             _to_append = pd.DataFrame(
                 {'ts': [curr_ts],
-                 'stack_output': [f'{self.basis_folder}/{subfolder_name}/{subfolder_name}.st'],
+                 'stack_output': [f'{self.basis_folder}/{subfolder_name}/{subfolder_name}.{self.output_ext}'],
                  'align_output': [f'{self.basis_folder}/{subfolder_name}/{subfolder_name}_ali.mrc']
                  },
             )
@@ -148,7 +149,7 @@ def _check_aligned_images(self):
     STACK CREATION
     """
 
-    def create_stack_folders(self):
+    def create_stack_folders(self, single_folder=False):
         """
         Method to create folders for storing stacked images.
         These folders will be used for alignment and reconstruction as well.
@@ -166,10 +167,17 @@ def create_stack_folders(self):
 
         # Create the folders and dictionary for future reference
         self._path_dict = {}
-        for curr_ts in self._process_list:
-            subfolder_path = f'{self.basis_folder}/{self.rootname}_{curr_ts:04}{self.suffix}'
+        if single_folder:
+            subfolder_path = f'{self.basis_folder}'
             os.makedirs(subfolder_path, exist_ok=True)
-            self._path_dict[curr_ts] = subfolder_path
+            for curr_ts in self._process_list:
+                self._path_dict[curr_ts] = subfolder_path
+        else:
+            for curr_ts in self._process_list:
+                subfolder_path = f'{self.basis_folder}/{self.rootname}_{curr_ts}{self.suffix}'
+                os.makedirs(subfolder_path, exist_ok=True)
+                self._path_dict[curr_ts] = subfolder_path
+
 
     def _sort_tilt_angles(self,
                           curr_ts: int
@@ -201,11 +209,10 @@ def create_rawtlt(self):
         (Note: Rather than grabbing info from file names as done in OTTERec,
                we use information directly from input metadata
         """
-
         for curr_ts in self._process_list:
             # 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:04}{self.params['System']['output_suffix']}.rawtlt")
+                           f"{curr_ts}{self.params['System']['output_suffix']}.rawtlt")
 
             # Sort the filtered metadata
             # Metadata is fetched in the _sort_tilt_angles method
@@ -239,7 +246,7 @@ def create_stack(self):
             # Create template for newstack
             self._filename_fileinlist = \
                 (f"{self._path_dict[curr_ts]}/{self.params['System']['output_rootname']}"
-                 f"_{curr_ts:04}{self.params['System']['output_suffix']}_sources.txt")
+                 f"_{curr_ts}{self.params['System']['output_suffix']}_sources.txt")
             self._stack_template = f"{len(meta_ts)}\n" + '\n0\n'.join(meta_ts['output']) + '\n0\n'
             with open(self._filename_fileinlist, 'w') as f:
                 f.write(self._stack_template)
@@ -287,8 +294,8 @@ def _get_adoc(self):
 
         # Template for directive file
         adoc_temp = """
-setupset.currentStackExt = st
-setupset.copyarg.stackext = st
+setupset.currentStackExt = <ext>
+setupset.copyarg.stackext = <ext>
 setupset.copyarg.dual = 0
 setupset.copyarg.userawtlt = <use_rawtlt>
 setupset.copyarg.pixel = <pixel_size>
@@ -300,9 +307,9 @@ def _get_adoc(self):
 runtime.Excludeviews.any.deleteOldFiles = <delete_old_files>
 runtime.Preprocessing.any.removeXrays = <remove_xrays>
 
-comparam.prenewst.newstack.BinByFactor = 1
+comparam.prenewst.newstack.BinByFactor = <aligned_bin_factor>
 
-runtime.AlignedStack.any.binByFactor = 1
+runtime.AlignedStack.any.binByFactor = <aligned_bin_factor>
 """
 
         fiducial_temp = """
@@ -362,19 +369,20 @@ def _get_adoc(self):
             adoc_temp = adoc_temp + patchtrack_temp
 
         convert_dict = {
+            'ext': self.params['System']['output_ext'],
             'use_rawtlt': 1 if self.params['BatchRunTomo']['setup']['use_rawtlt'] else 0,
-            'pixel_size': self.params['BatchRunTomo']['setup']['pixel_size'],
+            'pixel_size': self.params['BatchRunTomo']['setup']['pixel_size'] * self.params['BatchRunTomo']['setup']['stack_bin_factor'],
             'rot_angle': self.params['BatchRunTomo']['setup']['rot_angle'],
             'excl_views': "" if self.params["BatchRunTomo"]["setup"]["excluded_views"] == [0] \
             else f'{",".join(map(str, self.params["BatchRunTomo"]["setup"]["excluded_views"]))}',
             'gold_size': self.params['BatchRunTomo']['setup']['gold_size'] if fiducial else 0,
             'adoc_template': self.params['BatchRunTomo']['setup']['adoc_template'],
             'stack_bin_factor': self.params['BatchRunTomo']['setup']['stack_bin_factor'],
+            'aligned_bin_factor': self.params['BatchRunTomo']['setup']['aligned_bin_factor'],
 
             'delete_old_files': 1 if self.params['BatchRunTomo']['preprocessing']['delete_old_files'] else 0,
             'remove_xrays': 1 if self.params['BatchRunTomo']['preprocessing']['remove_xrays'] else 0,
 
-            'ca_bin_factor': self.params['BatchRunTomo']['coarse_align']['bin_factor'],
             'num_beads': self.params['BatchRunTomo']['setup']['num_beads'],
 
             'size_of_patches': f'{",".join(map(str, self.params["BatchRunTomo"]["patch_track"]["size_of_patches"]))}',
@@ -419,8 +427,8 @@ def _get_brt_align_command(self,
                '-CPUMachineList', f"{temp_cpu}",
                '-GPUMachineList', '1',
                '-DirectiveFile', './align.adoc',
-               '-RootName', self.params['System']['output_rootname'] + f'_{curr_ts:04}',
-               '-CurrentLocation', f'{self.basis_folder}/{self.rootname}_{curr_ts:04}{self.suffix}',
+               '-RootName', self.params['System']['output_rootname'] + f'_{curr_ts}',
+               '-CurrentLocation', f'{self.basis_folder}/{self.rootname}_{curr_ts}{self.suffix}',
                '-StartingStep', '0',
                '-EndingStep', '8',
                ]
@@ -508,19 +516,7 @@ def create_yaml(args_in=None):
     """
     Subroutine to create new yaml file for IMOD newstack / alignment
     """
-    # Parse user inputs
-    if args_in is None:  # default case, o2r.imod.new
-        logger = logMod.Logger(log_path="o2r_imod_align.log")
-        args = mgMod.get_args_align.show(run=True)
-    else:  # to create stacks for aretomo
-        args = args_in
-        logger = logMod.Logger(log_path="o2r_imod_stack_creation.log")
-
-    # Create the yaml file, then automatically update it
-    prmMod.new_align_yaml(args)
-    update_yaml(args, logger)
-
-    # logger(message="IMOD alignment metadata file created.")
+    mgMod.get_args_align.show(run=True)
 
 
 def update_yaml(args, logger):
@@ -531,8 +527,8 @@ def update_yaml(args, logger):
         args (Namespace): Namespace generated with user inputs
     """
     # Check if align and motioncorr yaml files exist
-    align_yaml_name = args.project_name.value + '_align.yaml'
-    mc2_yaml_name = args.project_name.value + '_mc2.yaml'
+    align_yaml_name = args.project_name + '_align.yaml'
+    mc2_yaml_name = args.project_name + '_mc2.yaml'
     if not os.path.isfile(align_yaml_name):
         logger(level="error",
                message="IMOD alignment config file not found.")
@@ -544,13 +540,13 @@ def update_yaml(args, logger):
 
     # Read in MC2 metadata (as Pandas dataframe)
     # We only need the TS number and the tilt angle for comparisons at this stage
-    mc2_md_name = args.project_name.value + '_mc2_mdout.yaml'
+    mc2_md_name = args.project_name + '_mc2_mdout.yaml'
     with open(mc2_md_name, 'r') as f:
         mc2_md = pd.DataFrame(yaml.load(f, Loader=yaml.FullLoader))[['ts']]
     # logger(message="MotionCor2 metadata read successfully.")
 
     # Read in previous alignment output metadata (as Pandas dataframe) for old projects
-    align_md_name = args.project_name.value + '_align_mdout.yaml'
+    align_md_name = args.project_name + '_align_mdout.yaml'
     if os.path.isfile(align_md_name):
         is_old_project = True
         with open(align_md_name, 'r') as f:
@@ -573,9 +569,9 @@ def update_yaml(args, logger):
 
     # Read in ctffind yaml file, modify, and update
     # read in MC2 yaml as well (some parameters depend on MC2 settings)
-    align_params = prmMod.read_yaml(project_name=args.project_name.value,
+    align_params = prmMod.read_yaml(project_name=args.project_name,
                                     filename=align_yaml_name)
-    mc2_params = prmMod.read_yaml(project_name=args.project_name.value,
+    mc2_params = prmMod.read_yaml(project_name=args.project_name,
                                   filename=mc2_yaml_name)
 
     align_params.params['System']['process_list'] = unique_ts_numbers
@@ -669,7 +665,7 @@ def run(newstack=False, do_align=True, ext=False, args_pass=None, exclusive=True
             args = parser.parse_args()
         project_name = args.project_name
     else:
-        project_name = args_in.project_name.value
+        project_name = args_in.project_name
 
     # Check if prerequisite files exist
     align_yaml = project_name + '_align.yaml'
@@ -782,7 +778,7 @@ def get_align_stats(exclusive=True, args_in=None):
 
     # Loop through folders, find data and append to dataframe
     for curr_ts in aligned_ts:
-        target_file_path = f"{folder_path}/{rootname}_{curr_ts:04d}{suffix}/taLocals.log"
+        target_file_path = f"{folder_path}/{rootname}_{curr_ts}{suffix}/taLocals.log"
         if not os.path.isfile(target_file_path):
             raise IOError("Error in Ot2Rec.main.get_align_stats: alignment log file (taLocals) not found.")
 

src/Ot2Rec/aretomo.py

@@ -30,6 +30,12 @@
 from . import magicgui as mgMod
 from . import params as prmMod
 from . import user_args as uaMod
+from . import mgui_imod_align as alignMGUI
+
+
+class asObject(object):
+    def __init__(self, dict_obj):
+        self.__dict__ = dict_obj
 
 
 class AreTomo:
@@ -86,7 +92,7 @@ def _get_internal_metadata(self):
                                                self.params['System']['process_list']))
         for curr_ts in self.params['System']['process_list']:
             subfolder = (f"{self.basis_folder}/"
-                         f"{self.rootname}_{curr_ts:04d}{self.suffix}")
+                         f"{self.rootname}_{curr_ts}{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()):
@@ -95,7 +101,7 @@ def _get_internal_metadata(self):
             self.md_out["aretomo_output_dir"][curr_ts] = subfolder
             self.md_out["aretomo_align_stats"][curr_ts] = (
                 f"{subfolder}/"
-                f"{self.rootname}_{curr_ts:04d}{self.suffix}.st.aln"
+                f"{self.rootname}_{curr_ts}{self.suffix}.st.aln"
             )
 
         if self.params["AreTomo_setup"]["out_imod"] != "N/A":
@@ -154,7 +160,7 @@ def _get_aretomo_recon_command(self, i):
         if self.params['AreTomo_setup']['aretomo_mode'] == 1:
             cmd.append('-Align')
             cmd.append('0')
-        
+
         if self.params['AreTomo_recon']['recon_algo'] == "WBP":
             # WBP
             cmd.append('-Wbp')
@@ -220,7 +226,7 @@ def _run_aretomo(self, i):
             output_mrc = self.params["AreTomo_setup"]["output_mrc"][i]
             self.sta[curr_ts] = (
                 f'{self.basis_folder}/'
-                f'{self.rootname}_{curr_ts:04d}{self.suffix}/'
+                f'{self.rootname}_{curr_ts}{self.suffix}/'
                 f'{os.path.splitext(os.path.basename(output_mrc))[0]}_Imod/'
             )
 
@@ -243,7 +249,7 @@ def export_metadata(self):
         Method to export metadata as yaml
         """
         # If STA files created, move to common folder
-        if self.params["AreTomo_setup"]["out_imod"] != "N/A": 
+        if self.params["AreTomo_setup"]["out_imod"] != "N/A":
             for ts in list(self.sta.keys()):
                 sta_ts_folder = (
                     f"{self.sta_folder}/{self.sta[ts].split(os.sep)[-2]}"
@@ -277,7 +283,7 @@ def _update_volz(args, aretomo_params):
                     in nm to automatically calculate VolZ. Currently sample_thickness \
                     = {args['sample_thickness']} and pixel_size = {args['pixel_size']}")
             aretomo_params.params["AreTomo_recon"]["volz"] = int(
-                (args["sample_thickness"] * args["pixel_size"] * 0.1) + 200   # factor of 0.1 because pixel_size in A
+                (10 * args["sample_thickness"] // args["pixel_size"]) + 200   # factor of 0.1 because pixel_size in A
             )
 
     # Reject volz and sample thickness values which are not -1 or >0
@@ -290,7 +296,7 @@ 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 = mgMod.get_args_align
+            args_in_align = alignMGUI.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"]
@@ -332,11 +338,11 @@ def _get_process_list(file_list, rootname, suffix, ext):
         st_bn = os.path.basename(st)
         if suffix != "":
             ts_list.append(
-                int(st_bn.split(f"{rootname}_")[1].split(f"_{suffix}{ext}")[0])
+                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])
+                st_bn.split(f"{rootname}_")[1].split(ext)[0][:-1]
             )
     return ts_list
 
@@ -507,13 +513,13 @@ def create_yaml(input_mgNS=None):
 
     # Parse user inputs
     if input_mgNS is None:
-        args = mgMod.get_args_aretomo.show(run=True).asdict()
+        _ = mgMod.get_args_aretomo.show(run=True)
     else:
         args = input_mgNS
 
-    # Create the yaml file, then automatically update it
-    prmMod.new_aretomo_yaml(args)
-    update_yaml(args)
+        # Create the yaml file, then automatically update it
+        prmMod.new_aretomo_yaml(args)
+        update_yaml(args)
 
 
 def run():