Put the lid on when plate is on B15

Author: danr

cellpainter/cellpainter/moves.py

@@ -213,7 +213,7 @@ def tags(self) -> list[str]:
                     out += [tag]
         return out
 
-    def expand_hotels(self, name: str) -> dict[str, MoveList]:
+    def expand_hotels(self, name: str, *, expand_base: bool) -> dict[str, MoveList]:
         '''
         If there is a tag like 19/21 then expand to all heights 1/21, 3/21, .., 21/21
         The first occurence of 19 in the name is replaced with 1, 3, .., 21, so
@@ -233,14 +233,22 @@ def expand_hotels(self, name: str) -> dict[str, MoveList]:
         else:
             raise ValueError(f'Unknown hotel in: {name}')
         for tag in set(self.tags()):
-            if m := re.match(r'(\d+)/(11|21)$', tag):
-                ref_h = int(m.group(1))
-                assert str(ref_h) in name
-                assert ref_h in hotel_locs
-                for h in hotel_locs:
-                    dz = (h - ref_h) * hotel_dist
-                    name_h = name.replace(str(ref_h), str(h), 1)
-                    out[name_h] = self.adjust_tagged(tag, dname=str(h), dz=dz)
+            if expand_base:
+                if tag == 'base 21':
+                    ref_h = 21
+                    for h in [15]:
+                        dz = (h - ref_h) * hotel_dist
+                        name_h = f'{name} [base B{h}]'
+                        out[name_h] = self.adjust_tagged(tag, dname=f'[base B{h}]', dz=dz)
+            if not expand_base:
+                if m := re.match(r'(\d+)/(11|21)$', tag):
+                    ref_h = int(m.group(1))
+                    assert str(ref_h) in name
+                    assert ref_h in hotel_locs
+                    for h in hotel_locs:
+                        dz = (h - ref_h) * hotel_dist
+                        name_h = name.replace(str(ref_h), str(h), 1)
+                        out[name_h] = self.adjust_tagged(tag, dname=str(h), dz=dz)
         return out
 
     def with_sections(self, include_Section: bool=False) -> list[tuple[str, Move]]:
@@ -467,7 +475,9 @@ def read_and_expand(filename: Path) -> dict[str, MoveList]:
     ml = MoveList.read_jsonl(filename)
     expanded = ml.expand_sections()
     for k, v in list(expanded.items()):
-        expanded |= v.expand_hotels(k)
+        expanded |= v.expand_hotels(k, expand_base=False)
+    for k, v in list(expanded.items()):
+        expanded |= v.expand_hotels(k, expand_base=True)
     return expanded
 
 def read_movelists() -> dict[str, MoveList]:
@@ -589,6 +599,7 @@ def effect(self, world: World) -> dict[str, str | None]:
 movelists = read_movelists()
 
 B21 = 'B21'
+B15 = 'B15'
 effects: dict[str, Effect] = {}
 
 for k, v in movelists.items():
@@ -613,6 +624,10 @@ def effect(self, world: World) -> dict[str, str | None]:
     effects[lid_Bi + ' get'] = PutLidOn(source=Bi, target=B21)
     effects[lid_Bi + ' put'] = TakeLidOff(source=B21, target=Bi)
 
+    lid_Bi = f'lid-B{i} [base B15]'
+    effects[lid_Bi + ' get'] = PutLidOn(source=Bi, target=B15)
+    effects[lid_Bi + ' put'] = TakeLidOff(source=B15, target=Bi)
+
 for k in list(effects.keys()):
     effects[k + ' transfer'] = effects[k]
 

cellpainter/cellpainter/protocol.py

@@ -41,7 +41,7 @@ class OptPrio:
     wash_to_disp  = Min(priority=6, weight=1)
     incu_slack    = Min(priority=6, weight=1)
     without_lid   = Min(priority=4, weight=1)
-    batch_time    = Min(priority=3, weight=1)
+    total_time    = Min(priority=3, weight=1)
     squeeze_steps = Min(priority=2, weight=1)
     inside_incu   = Max(priority=1, weight=0)
 
@@ -62,6 +62,10 @@ def lid_put(self):
     def lid_get(self):
         return f'lid-{self.lid_loc} get'
 
+    @property
+    def lid_get_base_B15(self):
+        return f'lid-{self.lid_loc} get [base B15]'
+
     @property
     def rt_put(self):
         return f'{self.rt_loc} put'
@@ -333,6 +337,21 @@ class ProtocolConfig:
     blue_prime: list[str]
     use_blue: bool
 
+    '''
+    def any_disp(self):
+        return any([
+            *[step.disp for step in self.steps],
+            *[step.disp_prime for step in self.steps],
+            *[step.disp_prep for step in self.steps],
+        ])
+
+    def any_wash(self):
+        return self.wash_prime or any([step.wash for step in self.steps])
+
+    def any_blue(self):
+        return self.use_blue or self.blue_prime or any([step.blue for step in self.steps])
+    '''
+
 from .protocol_paths import ProtocolPaths, paths_v5
 
 @dataclass(frozen=True)
@@ -462,15 +481,15 @@ def program_test_comm(with_incu: bool=True, with_blue: bool=True) -> Command:
     Test communication with robotarm, washer, dispenser and incubator.
     '''
     return Seq(
-        # BlueCmd(action='TestCommunications', protocol_path=None).fork() if with_blue else Idle(),
+        BlueCmd(action='TestCommunications', protocol_path=None).fork() if with_blue else Idle(),
         DispCmd(cmd='TestCommunications', protocol_path=None).fork(),
         IncuCmd(action='get_status', incu_loc=None).fork() if with_incu else Idle(),
         RobotarmCmd('ur gripper init and check'),
         WaitForResource('disp'),
         WashCmd(cmd='TestCommunications', protocol_path=None).fork(),
         WaitForResource('incu') if with_incu else Idle(),
         WaitForResource('wash'),
-        # WaitForResource('blue') if with_blue else Idle(),
+        WaitForResource('blue') if with_blue else Idle(),
     ).add(Metadata(step_desc='test comm'))
 
 Desc = tuple[str, str, str]
@@ -509,8 +528,12 @@ def paint_batch(batch: list[Plate], protocol_config: ProtocolConfig) -> Command:
         Checkpoint(f'batch {batch_index}'),
     ]
 
+    prep_cmds += [
+        program_test_comm(with_blue=p.use_blue),
+        BlueCmd('get_working_plate').fork() if p.use_blue else Idle(),
+    ]
+
     post_cmds = [
-        Duration(f'batch {batch_index}', OptPrio.batch_time),
     ]
 
     chunks: dict[Desc, Iterable[Command]] = {}
@@ -580,6 +603,13 @@ def paint_batch(batch: list[Plate], protocol_config: ProtocolConfig) -> Command:
                 ),
             ]
 
+            lid_on_base_B15 = [
+                *RobotarmCmds(
+                    plate_with_corrected_lid_pos.lid_get_base_B15,
+                    after_drop=[Duration(f'{plate_desc} lid off {ix}', OptPrio.without_lid)]
+                ),
+            ]
+
             if step.name == 'Mito' or step.name == 'PFA':
                 incu_get = [
                     # Idle() + 'sep {plate_desc} {step.name}',
@@ -676,7 +706,8 @@ def paint_batch(batch: list[Plate], protocol_config: ProtocolConfig) -> Command:
                             cmd.add(Metadata(plate_id=None))
                             for cmd in blue_prime
                             if plate is first_plate
-                            if not prev_step or not prev_step.blue
+                            # if not prev_step or not prev_step.blue
+                            if step.blue # let's just always prime blue for simplicity
                         ],
                         BlueCmd('Validate', step.blue),
                     ),
@@ -809,11 +840,11 @@ def blue_to_B(z: int):
             chunks[plate.id, step.name, 'blue -> B21' ] = [*blue_to_B(21), *lid_on]
             chunks[plate.id, step.name, 'blue -> B15' ] = [*blue_to_B(15)]
 
-            if 0 and step.name == 'Mito' and not step.blue and not step.wash:
-                # exception!
-                chunks[plate.id, step.name, 'disp -> B15' ] = [*disp_to_B(21), *lid_on, *RobotarmCmds('B15 put')]
+            if step.disp and not step.blue and not step.wash:
+                # put on the lid now
+                chunks[plate.id, step.name, 'disp -> B15' ] = [*disp_to_B(15), *lid_on_base_B15]
                 chunks[plate.id, step.name,  'B15 -> B21' ] = []
-                chunks[plate.id, step.name,  'B21 -> incu'] = [*B15_to_incu]
+                chunks[plate.id, step.name,  'B21 -> incu'] = [*RobotarmCmds('B15 get'), *B21_to_incu]
             else:
                 chunks[plate.id, step.name, 'disp -> B15' ] = [*disp_to_B(15)]
                 chunks[plate.id, step.name,  'B15 -> B21' ] = [*RobotarmCmds('B15 get'), *lid_on]
@@ -948,11 +979,9 @@ def cell_paint_program(batch_sizes: list[int], protocol_config: ProtocolConfig)
     program = Seq(*cmds)
     program = Seq(
         Checkpoint('run'),
-        program_test_comm(with_blue=protocol_config.use_blue),
-        BlueCmd('get_working_plate').fork() if protocol_config.use_blue else Idle(),
-        WaitForCheckpoint('run') + 'initialization slack',
+        # we now do test comm at start of each batch
         program,
-        Duration('run', OptPrio.batch_time)
+        Duration('run', OptPrio.total_time)
     )
     return Program(
         command=program,

cellpainter/cellpainter/protocol_vis.py

@@ -162,7 +162,7 @@ def index() -> Iterator[Tag | dict[str, str]]:
                     span(f'{delay_secs.value} s'),
                 ),
                 label(span('zoom: '), zoom_int.range(), span(str(zoom_int.value))),
-                label(span('pfa duration: '), pfa_duration.range().extend(width=200), span(f'{pfa_duration.value} s')),
+                # label(span('pfa duration: '), pfa_duration.range().extend(width=200), span(f'{pfa_duration.value} s')),
                 label(span('vertical: '), vertical.input().extend(style='justify-self: left')),
                 background='#fff',
                 border_bottom='1px #0008 solid',

cellpainter/cellpainter/small_protocols.py

@@ -139,7 +139,7 @@ def test_comm(_: SmallProtocolArgs):
     '''
     Test communication with robotarm, washer, dispenser and incubator.
     '''
-    return Program(protocol.program_test_comm().add(Metadata(gui_force_show=True)))
+    return Program(protocol.program_test_comm(with_blue=False).add(Metadata(gui_force_show=True)))
 
 @ur_protocols.append
 def test_circuit(args: SmallProtocolArgs):

cellpainter/movelists/lid-B19.jsonl

@@ -1,10 +1,11 @@
 {"type":"Section","section":"lid-B19 put"}
 {"type":"MoveJoint","joints":[94.88,-110.59,90.31,19.45,95.29,179.84],"name":"B neu"}
-{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"name":"B21 neu"}
-{"type":"MoveLin","xyz":[199.7,-566.9,821.9],"rpy":[0.0,0.7,89.6],"name":"B21 pick","slow":true}
+{"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 entrance"}
+{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 neu"}
+{"type":"MoveLin","xyz":[199.7,-566.9,821.9],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 pick","slow":true}
 {"type":"GripperMove","pos":255}
-{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"name":"B21 neu"}
-{"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.7,89.6],"name":"B21 entrance"}
+{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 neu"}
+{"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 entrance"}
 {"type":"MoveLin","xyz":[199.7,-421.8,751.1],"rpy":[0.0,0.7,89.6],"tag":"19/21","name":"B19 entrance"}
 {"type":"MoveLin","xyz":[199.7,-567.4,751.1],"rpy":[0.0,0.7,89.6],"tag":"19/21","name":"B19 neu"}
 {"type":"MoveLin","xyz":[199.7,-567.4,742.6],"rpy":[0.0,0.7,89.6],"tag":"19/21","name":"B19 drop","slow":true}
@@ -20,9 +21,10 @@
 {"type":"GripperMove","pos":255}
 {"type":"MoveLin","xyz":[199.7,-567.4,751.1],"rpy":[0.0,0.7,89.6],"tag":"19/21","name":"B19 pick neu"}
 {"type":"MoveLin","xyz":[199.7,-421.8,751.1],"rpy":[0.0,0.7,89.6],"tag":"19/21","name":"B19 entrance"}
-{"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.7,89.6],"name":"B21 entrance"}
-{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"name":"B21 neu"}
-{"type":"MoveLin","xyz":[199.7,-566.9,822.2],"rpy":[0.0,0.7,89.6],"name":"B21 drop","slow":true}
+{"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 entrance"}
+{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 neu"}
+{"type":"MoveLin","xyz":[199.7,-566.9,822.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 drop","slow":true}
 {"type":"GripperMove","pos":88}
-{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"name":"B21 neu"}
+{"type":"MoveLin","xyz":[199.7,-566.9,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 neu"}
+{"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.7,89.6],"tag":"base 21","name":"B21 entrance"}
 {"type":"MoveLin","xyz":[199.7,-421.7,834.2],"rpy":[0.0,0.8,89.6],"name":"B neu"}