dev(process): adapt to cleaner API for image processing. Some cleanup and mypy.

Author: grololo06

src/Background.py

@@ -205,6 +205,9 @@ def adaptative_upload(
         meta_for_scan = find_scan_metadata(
             all_scans_meta, self.sample_name, self.scan_name
         )
+        assert (
+            meta_for_scan is not None
+        ), f"Not found, line for {self.sample_name} in {self.zoo_project.name} metadata"
         acq_orig_id = meta_for_scan["fracid"] + "_" + self.sample_name
         # Get all acquisitions for project
         all_acqs: List[AcquisitionModel] = client.list_acquisitions(dst_project_id)

src/img_proc/process.py

@@ -177,7 +177,7 @@ def convert_scan_and_backgrounds(
 ):
     logger.info(f"Converting backgrounds")
     bg_converted_files = [
-        processor.converter.do_file_to_image(a_raw_bg_file)
+        processor.converter.do_file_to_image(a_raw_bg_file, True)
         for a_raw_bg_file in bg_scans
     ]
     logger.info(f"Combining backgrounds")
@@ -187,7 +187,7 @@ def convert_scan_and_backgrounds(
     # Scan pre-processing
     logger.info(f"Converting scan")
     eight_bit_scan_image, scan_resolution = processor.converter.do_file_to_image(
-        raw_scan
+        raw_scan, False
     )
     # Background removal
     logger.info(f"Removing background")

src/modern/jobs/VerifiedSepToUpload.py

@@ -521,7 +521,7 @@ async def get_subsample_scan(
             raw_sample_file = zoo_project.zooscan_scan.raw.get_file(
                 subsample_name, THE_SCAN_PER_SUBSAMPLE
             )
-            processor.converter.do_file_to_file(raw_sample_file, real_file)
+            processor.converter.do_file_to_file(raw_sample_file, real_file, False)
     else:
         real_files: List[Path] = list(
             filter(