Account for CTF translations

nabu/app/fullfield_mixed.py

@@ -322,8 +322,8 @@ class FullRadiosPipeline(FullFieldPipeline):
             self.phase_retrieval.retrieve_phase(
                 self.radios[i],
                 padding_mode=padding_mode,
-                translation_vh=None,
-                normalize_by_mean=None,
+                translation_vh=self.dataset_info.ctf_translations[i],
+                normalize_by_mean=options["ctf_normalize_by_mean"],
             )
 
 

nabu/resources/dataset_analyzer.py

@@ -100,6 +100,7 @@ class DatasetAnalyzer(object):
         self.radio_dims = (self.dataset_scanner.dim_1, self.dataset_scanner.dim_2)
         self._binning = (1, 1)
         self.translations = None
+        self.ctf_translations = None
         self.axis_position = None
         self._radio_dims_notbinned = self.radio_dims
 

nabu/resources/dataset_validator.py

@@ -37,7 +37,8 @@ class NabuValidator(object):
         self.convert_negative_indices()
         self.get_angles()
         self._get_rotation_axis()
-        self._get_translation_file()
+        self._get_translation_file("reconstruction", "translation_movements_file", "translations")
+        self._get_translation_file("phase", "ctf_translations_file", "ctf_translations")
         self._get_resources()
         self._get_output_filename()
 
@@ -130,9 +131,8 @@ class NabuValidator(object):
         self.dataset_infos.axis_correction = axis_correction
 
 
-    def _get_translation_file(self):
-        rec_params = self.nabu_config["reconstruction"]
-        transl_file = rec_params["translation_movements_file"]
+    def _get_translation_file(self, config_section, config_key, dataset_info_attr):
+        transl_file = self.nabu_config[config_section][config_key]
         if transl_file in (None, ''):
             return
         translations = None
@@ -150,7 +150,7 @@ class NabuValidator(object):
             except:
                 print("Something wrong with translation_movements_file %s" % transl_file)
                 raise
-        self.dataset_infos.translations = translations
+        setattr(self.dataset_infos, dataset_info_attr, translations)
 
 
     def _get_resources(self):

nabu/resources/nabu_config.py

@@ -208,7 +208,7 @@ nabu_config = {
             "validator": optional_string_validator,
             "type": "optional",
         },
-        "ctf_translations": {
+        "ctf_translations_file": {
             "default": "",
             "help": "A file where each line has two values: horizontal and vertical displacements. There should be as many values as there are projection images.",
             "validator": optional_file_location_validator,

nabu/resources/processconfig.py

@@ -417,4 +417,3 @@ class ProcessConfig:
         phase_options["ctf_lim1"] = ctf_advanced_params["lim1"]
         phase_options["ctf_lim2"] = ctf_advanced_params["lim2"]
         phase_options["ctf_normalize_by_mean"] = ctf_advanced_params["normalize_by_mean"]
-        phase_options["ctf_translations"] = user_phase_options["ctf_translations"]