Admin clone/transform tool: add support for XYZ offsets in transformation

Author: tomka

django/applications/catmaid/control/annotationadmin.py

@@ -76,6 +76,10 @@ class TransformImportForm(forms.Form):
         queryset=Stack.objects.all())
     x_factor = forms.FloatField(initial=1.0, required=False, help_text="A factor that is multiplied to each X shift")
     y_factor = forms.FloatField(initial=1.0, required=False, help_text="A factor that is multiplied to each Y shift")
+    z_factor = forms.FloatField(initial=1.0, required=False, help_text="A factor that is multiplied to each Z shift")
+    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")
     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',
@@ -323,6 +327,10 @@ def done(self, form_list, **kwargs) -> HttpResponse:
         reference_stack = transform_data['reference_stack']
         x_factor = transform_data['x_factor']
         y_factor = transform_data['y_factor']
+        z_factor = transform_data['z_factor']
+        x_offset = transform_data['x_offset']
+        y_offset = transform_data['y_offset']
+        z_offset = transform_data['z_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')
@@ -332,8 +340,9 @@ def done(self, form_list, **kwargs) -> HttpResponse:
             if transform_data_type == 'csv-z-slices':
                 with StringIO(transform_text) as transform_stream:
                     reader = csv.reader(transform_stream, delimiter=delimiter)
-                    transform = list(map(lambda xy: [x_factor * float(xy[0]),
-                                                     y_factor * float(xy[1])],
+                    transform = list(map(lambda xy: [x_factor * float(xy[0]) + x_offset,
+                                                     y_factor * float(xy[1]) + y_offset,
+                                                     z_offset],
                                         reader))
             else:
                 raise ValidationError(f"Unknown transform data type: {transform_data_type}")

django/applications/catmaid/control/importer.py

@@ -1749,10 +1749,11 @@ def transform_single_location(self, location, clamped_locations):
             z_index = int(location.location_z / self.reference_stack.resolution.z)
             if z_index >= len(self.transform) or z_index < 0:
                 clamped_locations[z_index] += 1
-                z_index = len(self.transform) - 1
-            xy_shift = self.transform[z_index]
-            location.location_x += xy_shift[0]
-            location.location_y += xy_shift[1]
+                z_index = 0 if z_index < 0 else len(self.transform) - 1
+            xyz_shift = self.transform[z_index]
+            location.location_x += xyz_shift[0]
+            location.location_y += xyz_shift[1]
+            location.location_z += xyz_shift[2]
 
         return location
 
@@ -1779,10 +1780,11 @@ def transform_volume(self, volume, clamped_locations):
                     z_index = int(c[2] / self.reference_stack.resolution.z)
                     if z_index >= len(self.transform) or z_index < 0:
                         clamped_locations[z_index] += 1
-                        z_index = len(self.transform) - 1
-                    xy_shift = self.transform[z_index]
-                    c[0] += xy_shift[0]
-                    c[1] += xy_shift[1]
+                        z_index = 0 if z_index < 0 else len(self.transform) - 1
+                    xyz_shift = self.transform[z_index]
+                    c[0] += xyz_shift[0]
+                    c[1] += xyz_shift[1]
+                    c[2] += xyz_shift[2]
 
             # Convert array to TIN WKT again
             wkt_data = 'TIN Z (' + ','.join(map(lambda t: '((' + ','.join(list(map(lambda c: ' '.join(list(map(str, c))), t))) + '))', triangles)) + ')'