Persisted containers xy are center (#143)

* container files' XY reference center of Well, not lower-left corner

* updated tests

* added 'type' to calibration delta

* checking calibration data version and overwriting with blank file if version doesn't match

* fixes saving and leading new calibration json

* fixes tests

* overwrites file instead of appending to; checks for 'data' key in calibrations file

* removes print statement

* adds tests to vector

Author: andySigler

opentrons/containers/calibrator.py

@@ -67,6 +67,7 @@ def calibrate(self,
             current = children[name]
 
         current['delta'] = delta
+        current['type'] = placeable.get_type()
         self.calibration_data = calibration_data
 
         self._apply_calibration(calibration_data, self.root_placeable)

opentrons/containers/persisted_containers.py

@@ -184,6 +184,12 @@ def create_container_obj_from_dict(container_data: dict) -> Container:
 
         well = Well(properties=well_properties)
 
+        # subtract half the size, because
+        # Placeable assigns X-Y to bottom-left corner, but
+        # persisted container files assign X-Y to center of each Well
+        x -= (well.x_size() / 2)
+        y -= (well.y_size() / 2)
+
         well_coordinates = (
             x + origin_offset_x,
             y + origin_offset_y,

opentrons/containers/placeable.py

@@ -135,6 +135,12 @@ def get_name(self):
 
         return self.parent.children_by_reference[self]
 
+    def get_type(self):
+        """
+        Returns the Placeable's type or class name
+        """
+        return self.properties.get('type', self.__class__.__name__)
+
     def get_children_list(self):
         """
         Returns the list of children in the order they were added

opentrons/instruments/instrument.py

@@ -28,6 +28,9 @@ class Instrument(object):
     It gives the instruments ability to CRUD their calibration data,
     and gives access to some common methods across instruments
     """
+
+    calibration_data_version = 1
+
     calibration_key = "unique_name"
     persisted_attributes = []
     persisted_defaults = {}
@@ -121,18 +124,18 @@ def init_calibrations(self, key, attributes=None):
         if not os.path.isdir(self._get_calibration_dir()):
             os.mkdir(self._get_calibration_dir())
 
-        file_path = self._get_calibration_file_path()
-        if not os.path.isfile(file_path):
-            with open(file_path, 'a') as f:
-                f.write(json.dumps({}))
+        if not os.path.isfile(self._get_calibration_file_path()):
+            self._write_blank_calibrations_file()
+        else:
+            self._check_calibrations_version()
 
     def update_calibrations(self):
         """
         Saves the instrument's peristed attributes to file
         """
         last_persisted_data = self._read_calibrations()
 
-        last_persisted_data[self.calibration_key] = (
+        last_persisted_data['data'][self.calibration_key] = (
             self._strip_vector(
                 self._build_calibration_data())
         )
@@ -161,14 +164,22 @@ def delete_calibration_data(self):
             setattr(self, key, val)
         self.update_calibrations()
 
-    def delete_calibration_file(self):
+    def _delete_calibration_file(self):
         """
         Deletes the entire calibrations file
         """
         file_path = self._get_calibration_file_path()
         if os.path.exists(file_path):
             os.remove(file_path)
 
+    def _write_blank_calibrations_file(self):
+        self._delete_calibration_file()
+        with open(self._get_calibration_file_path(), 'w') as f:
+            f.write(json.dumps({
+                'version': self.calibration_data_version,
+                'data': {}
+            }))
+
     def _get_calibration_dir(self):
         """
         :return: the directory to save calibration data
@@ -186,7 +197,8 @@ def _get_calibration(self):
         """
         :return: this instrument's saved calibrations data
         """
-        return self._read_calibrations().get(self.calibration_key)
+        data = self._read_calibrations()['data']
+        return data.get(self.calibration_key)
 
     def _build_calibration_data(self):
         """
@@ -206,9 +218,25 @@ def _read_calibrations(self):
             try:
                 loaded_json = json.load(f)
             except json.decoder.JSONDecodeError:
-                loaded_json = {}
+                self._write_blank_calibrations_file()
+                return self._read_calibrations()
             return self._restore_vector(loaded_json)
 
+    def _check_calibrations_version(self):
+        """
+        Read calibration file, and checks for version number
+        If no version number, file is replaced with version number
+        """
+        with open(self._get_calibration_file_path()) as f:
+            try:
+                file = json.load(f)
+                version = file.get('version')
+                data = file.get('data')
+                if not version or not data or len(file.keys()) > 2:
+                    self._write_blank_calibrations_file()
+            except json.decoder.JSONDecodeError:
+                self._write_blank_calibrations_file()
+
     def _strip_vector(self, obj, root=True):
         """
         Iterates through a dictionary, converting Vector classes

tests/opentrons/containers/test_calibrator.py

@@ -27,17 +27,21 @@ def test_apply_calibration(self):
         calibration_data = {
             'A1':
             {
+                'type': 'Slot',
                 'delta': (1, 1, 1),
                 'children': {
                     'tube_rack': {
+                        'type': 'tube-rack-2ml',
                         'delta': (1, 1, 1),
                         'children': {
                             'Red':
                             {
+                                'type': 'Well',
                                 'delta': (1, 1, 1)
                             },
                             'Blue':
                             {
+                                'type': 'Well',
                                 'delta': (2, 2, 2)
                             }
                         }
@@ -62,17 +66,21 @@ def test_convert(self):
         calibration_data = {
             'A1':
             {
+                'type': 'Slot',
                 'delta': (1, 1, 1),
                 'children': {
                     'tube_rack': {
+                        'type': 'tube-rack-2ml',
                         'delta': (1, 1, 1),
                         'children': {
                             'Red':
                             {
+                                'type': 'Well',
                                 'delta': (1, 1, 1)
                             },
                             'Blue':
                             {
+                                'type': 'Well',
                                 'delta': (2, 2, 2)
                             }
                         }
@@ -108,7 +116,8 @@ def test_calibrate(self):
             'A1': {
                 'children': {
                     'tube_rack': {
-                        'delta': (-1.0, -1.0, -1.0)
+                        'delta': (-1.0, -1.0, -1.0),
+                        'type': 'Container'
                     }
                 }
             }

tests/opentrons/containers/test_grid.py

@@ -29,8 +29,8 @@ def test_rows_cols(self):
 
     def test_placeable(self):
         plate = self.plate
-        self.assertEqual(plate.rows[0].center(plate), (14.44, 17.54, 5.25))
-        self.assertEqual(plate.rows[1].center(plate), (14.44, 26.54, 5.25))
+        self.assertEqual(plate.rows[0].center(plate), (11.24, 14.34, 5.25))
+        self.assertEqual(plate.rows[1].center(plate), (11.24, 23.34, 5.25))
         self.assertEqual(plate.rows[0].center(plate),
                          plate.cols[0].center(plate))
 

tests/opentrons/containers/test_persisted_containers.py

@@ -71,8 +71,8 @@ def test_load_persisted_container(self):
         well_1 = wells[0]
         well_2 = wells[1]
 
-        self.assertEqual(well_1.coordinates(), (13.67 + 0, 16.0 + 0, 0))
-        self.assertEqual(well_2.coordinates(), (13.67 + 0, 16.0 + 19.3, 0))
+        self.assertEqual(well_1.coordinates(), (5.86 + 0, 8.19 + 0, 0))
+        self.assertEqual(well_2.coordinates(), (5.86 + 0, 8.19 + 19.3, 0))
 
     def test_load_all_persisted_containers(self):
         all_persisted_containers = \
@@ -121,5 +121,5 @@ def test_create_container_obj_from_dict(self):
         well_1 = wells[0]
         well_2 = wells[1]
 
-        self.assertEqual(well_1.coordinates(), (13.3 + 0, 17.5 + 0, 0))
-        self.assertEqual(well_2.coordinates(), (13.3 + 0, 17.5 + 19.3, 0))
+        self.assertEqual(well_1.coordinates(), (5.49 + 0, 9.69 + 0, 0))
+        self.assertEqual(well_2.coordinates(), (5.49 + 0, 9.69 + 19.3, 0))

tests/opentrons/labware/test_crud_calibrations.py

@@ -38,7 +38,8 @@ def test_save_load_calibration_data(self):
         self.p200 = instruments.Pipette(name="p200", axis="b")
 
         expected_delta = {
-            'delta': (1.0, 2.0, 3.0)
+            'delta': (1.0, 2.0, 3.0),
+            'type': '96-flat'
         }
 
         self.assertTrue('A1' in self.p200.calibration_data)
@@ -52,7 +53,8 @@ def test_delete_calibrations_data(self):
         self.p200 = instruments.Pipette(name="p200", axis="b")
 
         expected_delta = {
-            'delta': (1.0, 2.0, 3.0)
+            'delta': (1.0, 2.0, 3.0),
+            'type': '96-flat'
         }
 
         self.assertTrue('A1' in self.p200.calibration_data)

tests/opentrons/labware/test_pipette.py

@@ -128,7 +128,8 @@ def test_calibrate_placeable(self):
             'A2': {
                 'children': {
                     '96-flat': {
-                        'delta': (1.0, 2.0, 3.0)
+                        'delta': (1.0, 2.0, 3.0),
+                        'type': '96-flat'
                     }}}}
 
         self.assertDictEqual(

tests/opentrons/util/test_vector.py

@@ -1,6 +1,6 @@
 import unittest
 
-from opentrons.util.vector import (Vector, VectorEncoder)
+from opentrons.util.vector import (Vector, VectorEncoder, VectorValue)
 import json
 
 
@@ -23,6 +23,17 @@ def test_add(self):
 
         self.assertEqual(res, Vector(5, 7, 9))
 
+    def test_to_iterable(self):
+
+        v1 = Vector(1, 2, 3)
+        iterable = v1.to_iterable()
+        self.assertTrue(hasattr(iterable, '__iter__'))
+
+    def test_zero_coordinates(self):
+
+        zero_coords = Vector(1, 2, 3).zero_coordinates()
+        self.assertEquals(zero_coords, VectorValue(0, 0, 0))
+
     def test_substract(self):
         v1 = Vector(1, 2, 3)
         v2 = Vector(4, 5, 6)