Admin clone/transform tool: add transform Z lookup offset

This allows to start using a transformation table only at a particular Z
index.

Author: tomka

django/applications/catmaid/control/annotationadmin.py

@@ -82,6 +82,7 @@ class TransformImportForm(forms.Form):
     x_offset = forms.FloatField(initial=0.0, required=False, help_text="A offset that is added to each X shift")
     y_offset = forms.FloatField(initial=0.0, required=False, help_text="A offset that is added to each Y shift")
     z_offset = forms.FloatField(initial=0.0, required=False, help_text="A offset that is added to each Z shift")
+    z_lookup_offset = forms.IntegerField(initial=0, required=False, help_text="An offset that is added to each Z look-up index. Slices before won't be transformed.")
     delimiter = forms.CharField(initial=',', required=False, help_text="The delimiter used in the transform CSV")
     transform_type = forms.ChoiceField(choices=TRANSFORM_TYPE_CHOICES, required=True, help_text="The type of tranformaton")
     transform_text = forms.CharField(widget=forms.Textarea, label='Transform',
@@ -204,6 +205,7 @@ def async_project_copy_job(import_task_id) -> str:
                         import_options['transform'] = scd['transform']
                         import_options['reference_stack_id'] = scd['reference_stack_id']
                         import_options['transform_in_project_space'] = scd['transform_in_project_space']
+                        import_options['transform_z_lookup_offset'] = scd['transform_z_lookup_offset']
 
                     # Import project data into new project
                     task_logger.info(f'Importing into project {target_project}')
@@ -343,6 +345,7 @@ def done(self, form_list, **kwargs) -> HttpResponse:
         x_offset = transform_data['x_offset']
         y_offset = transform_data['y_offset']
         z_offset = transform_data['z_offset']
+        z_lookup_offset = transform_data['z_lookup_offset']
         delimiter = transform_data['delimiter']
         transform_data_type = transform_data['transform_type']
         transform_text = transform_data['transform_text'].replace('\r\n', '\n').replace('\r', '\n')
@@ -380,6 +383,7 @@ def done(self, form_list, **kwargs) -> HttpResponse:
                     'reference_stack_id': reference_stack.id,
                     'transfer_stats': transfer_stats,
                     'transform_in_project_space': transform_data['transform_in_project_space'],
+                    'transform_z_lookup_offset': transform_data['z_lookup_offset'],
                 })
 
         # Make sure the created import task is available

django/applications/catmaid/control/importer.py

@@ -1468,6 +1468,7 @@ def __init__(self, source, target, user, options, custom_logger=None):
         reference_stack_id = options.get('reference_stack_id')
         self.reference_stack = Stack.objects.get(id=reference_stack_id) if reference_stack_id is not None else None
         self.transform_in_project_space = options.get('transform_in_project_space', False)
+        self.transform_z_lookup_offset = options.get('transform_z_lookup_offset', 0)
         self.precomputed_stats = options.get('precomputed_stats')
 
         # Map user IDs to newly created users
@@ -1750,10 +1751,13 @@ def transform_single_location(self, location, clamped_locations):
         """
         if self.transform and self.reference_stack:
             # Assume csv-z-slice type for now
-            z_index = int(location.location_z / self.reference_stack.resolution.z)
+            z_index = int(location.location_z / self.reference_stack.resolution.z) \
+                    + self.transform_z_lookup_offset
+            # Don't transform data outside of transform index
             if z_index >= len(self.transform) or z_index < 0:
                 clamped_locations[z_index] += 1
-                z_index = 0 if z_index < 0 else len(self.transform) - 1
+                return location
+
             xyz_shift = self.transform[z_index]
             if self.transform_in_project_space:
                 location.location_x += xyz_shift[0] * self.reference_stack.resolution.x
@@ -1786,10 +1790,12 @@ def transform_volume(self, volume, clamped_locations):
             for triangle_coords in triangles:
                 for c in triangle_coords:
                     # Assume csv-z-slice type for now
-                    z_index = int(c[2] / self.reference_stack.resolution.z)
+                    z_index = int(c[2] / self.reference_stack.resolution.z) \
+                            + self.transform_z_lookup_offset
                     if z_index >= len(self.transform) or z_index < 0:
                         clamped_locations[z_index] += 1
-                        z_index = 0 if z_index < 0 else len(self.transform) - 1
+                        continue
+
                     xyz_shift = self.transform[z_index]
                     if self.transform_in_project_space:
                         c[0] += xyz_shift[0] * self.reference_stack.resolution.x