Merge branch 'fix_translations' into 'master'

Fix horizontal/vertical translations in pipeline

Closes #299 and #300

See merge request !175

nabu/__init__.py

-__version__ = "2022.1.1"
+__version__ = "2022.1.2"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/pipeline/fullfield/grouped.py

@@ -264,6 +264,8 @@ class GroupedPipeline(ChunkedPipeline):
     def _init_ctf_phase(self):
         options = self.processing_options["phase"]
 
+        translations_vh = getattr(self.dataset_info, "ctf_translations", None)
+
         geo_pars_params = options["ctf_geo_pars"].copy()
         geo_pars_params["logger"] = self.logger
         geo_pars = GeoPars(**geo_pars_params)
@@ -277,6 +279,7 @@ class GroupedPipeline(ChunkedPipeline):
             fftw_num_threads=None, # TODO tune in advanced params of nabu config file
             use_rfft=True,
             normalize_by_mean=options["ctf_normalize_by_mean"],
+            translation_vh=translations_vh,
         )
 
 

nabu/pipeline/fullfield/grouped_cuda.py

@@ -62,7 +62,8 @@ class CudaGroupedPipeline(GroupedPipeline):
 
 
     # overwrite
-    def _init_ctf_phase(self):
+    def _init_ctf_phase(self):	
+        translations_vh = getattr(self.dataset_info, "ctf_translations", None)
         options = self.processing_options["phase"]
         geo_pars_params = options["ctf_geo_pars"].copy()
         geo_pars_params["logger"] = self.logger
@@ -75,6 +76,7 @@ class CudaGroupedPipeline(GroupedPipeline):
             lim2=options["ctf_lim2"],
             logger=self.logger,
             normalize_by_mean=options["ctf_normalize_by_mean"],
+            translation_vh=translations_vh,
         )
 
 

nabu/pipeline/fullfield/processconfig.py

@@ -56,6 +56,12 @@ class ProcessConfig(ProcessConfigBase):
                 print("Something wrong with translation_movements_file %s" % transl_file)
                 raise
         setattr(self.dataset_info, dataset_info_attr, translations)
+        if translations is not None:
+            # Horizontal translations are handled by "axis_correction" in backprojector
+            horizontal_translations = translations[:, 0]
+            if np.max(np.abs(horizontal_translations)) > 1e-3:
+                self.dataset_info.axis_correction = horizontal_translations
+
 
     def _get_rotation_axis_position(self):
         super()._get_rotation_axis_position()