enh: prepare for monarch exp

NSLS-II-BMM · Apr 13, 2024 · ffb5b30 · ffb5b30
1 parent 144447b
commit ffb5b30
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Showing 7 changed files with 239 additions and 17 deletions.
diff --git a/bmm_agents/monarch_pdf_subject.py b/bmm_agents/monarch_pdf_subject.py
@@ -6,31 +6,45 @@
 from bluesky_adaptive.server import register_variable
 from numpy.typing import ArrayLike
 
-from .sklearn import MultiElementActiveKmeansAgent
+from .sklearn import ActiveKmeansAgent
 
 logger = logging.getLogger(__name__)
 
 
-class KMeansMonarchSubject(MonarchSubjectAgent, MultiElementActiveKmeansAgent):
+class KMeansMonarchSubject(MonarchSubjectAgent, ActiveKmeansAgent):
     def __init__(
         self,
         *args,
         pdf_origin: Tuple[float, float],
         **kwargs,
     ):
         self.pdf_origin = np.array(pdf_origin)
+        self._pdf_control = False
         super().__init__(*args, **kwargs)
 
     @property
     def name(self):
-        return "KMeansPDFMonarchBMMSubject"
+        return "{self.analyzed_element}-KMeansPDFMonarchBMMSubject"
+
+    @property
+    def pdf_control(self):
+        return self._pdf_control
+
+    @pdf_control.setter
+    def pdf_control(self, value):
+        if value in {True, "true", "True", "TRUE", 1}:
+            self.pdf_control = True
+        else:
+            self.pdf_control = False
 
     def server_registrations(self) -> None:
         register_variable("pdf_origin", self, "pdf_origin")
+        self._register_property("pdf_control")
         return super().server_registrations()
 
     def subject_measurement_plan(self, relative_point: ArrayLike) -> Tuple[str, List, Dict]:
-        return "agent_redisAware_PDFcount", [relative_point + self.pdf_origin[0]], {}
+        point = relative_point + self.pdf_origin
+        return "agent_move_and_measure_hanukkah23", [], {"x": point[0], "y": point[1], "exposure": 30}
 
     def subject_ask(self, batch_size: int) -> Tuple[Sequence[Dict[str, ArrayLike]], Sequence[ArrayLike]]:
         suggestions, centers = self._sample_uncertainty_proxy(batch_size)
@@ -50,4 +64,4 @@ def subject_ask(self, batch_size: int) -> Tuple[Sequence[Dict[str, ArrayLike]],
         return docs, suggestions
 
     def subject_ask_condition(self):
-        return True
+        return self.pdf_control
diff --git a/bmm_agents/sklearn.py b/bmm_agents/sklearn.py
@@ -18,7 +18,7 @@
 
 class PassiveKmeansAgent(BMMBaseAgent, ClusterAgentBase):
     def __init__(self, k_clusters, analyzed_element, *args, **kwargs):
-        estimator = KMeans(k_clusters)
+        estimator = KMeans(k_clusters, n_init="auto")
         _default_kwargs = self.get_beamline_objects()
         _default_kwargs.update(kwargs)
 

diff --git a/bmm_agents/startup_scripts/mmm5-tax-day/Ni_KmeansMonarch.py b/bmm_agents/startup_scripts/mmm5-tax-day/Ni_KmeansMonarch.py
@@ -0,0 +1,90 @@
+import logging
+import os
+
+import numpy as np
+import tiled.client.node  # noqa: F401
+from bluesky_adaptive.server import register_variable, shutdown_decorator, startup_decorator
+from pdf_agents.agents import PDFBaseAgent
+
+from bmm_agents.monarch_pdf_subject import KMeansMonarchSubject
+
+logger = logging.getLogger(__name__)
+
+
+beamline_objects = KMeansMonarchSubject.get_beamline_objects()
+beamline_objects["qserver"].set_authorization_key(api_key=os.getenv("HTTPSERVER_API_KEY", "zzzzz"))
+
+pdf_objects = PDFBaseAgent.get_beamline_objects()
+pdf_objects["qserver"].set_authorization_key(api_key=os.getenv("HTTPSERVER_API_KEY", "yyyyy"))
+
+old_mmm4_origin = [[186.307, 89.276], [186.384, 89.305]]
+new_mmm5_origin = [[174.550, 103.806], [175.127, 103.484]]
+
+agent = KMeansMonarchSubject(
+    filename="PtNi-Multimodal-PtDrivenKmeans",
+    exp_mode="fluorescence",
+    read_mode="transmission",
+    exp_data_type="mu",
+    elements=["Pt", "Ni"],
+    edges=["L3", "K"],
+    element_origins=new_mmm5_origin,
+    element_det_positions=[180, 110],
+    sample="AlPtNi wafer pretend-binary PtNi",
+    preparation="AlPtNi codeposited on a silica wafer",
+    exp_bounds="-200 -30 -10 25 13k",
+    exp_steps="10 2 0.3 0.05k",
+    exp_times="1 1 1 1",
+    # PDF Args
+    subject_qserver=pdf_objects["qserver"],
+    subject_kafka_producer=pdf_objects["kafka_producer"],
+    subject_endstation_key="pdf",
+    pdf_origin=(-128.85, 49.91),
+    # Active Kmeans Args
+    bounds=np.array([(-30, 30), (-30, 30)]),
+    # BS Adaptive Args
+    ask_on_tell=False,
+    report_on_tell=True,
+    k_clusters=4,
+    analyzed_element="Ni",
+    queue_add_position="back",
+    **beamline_objects
+)
+
+
+def load_uids(path):
+    with open(path, "r") as f:
+        uids = []
+        for line in f:
+            uid = line.strip().strip(",").strip("'")
+            if agent.trigger_condition(uid):
+                uids.append(uid)
+    return uids
+
+
+@startup_decorator
+def startup():
+    agent.start()
+    path = (
+        "/nsls2/data/bmm/shared/config/source/bmm-agents/"
+        "bmm_agents/startup_scripts/mmm5-tax-day/historical_mmm4_uids.txt"
+    )
+    uids = load_uids(path)
+
+    agent.element_origins = old_mmm4_origin
+    agent.tell_agent_by_uid(uids)
+    agent.element_origins = new_mmm5_origin
+
+    path = (
+        "/nsls2/data/bmm/shared/config/source/bmm-agents/" "bmm_agents/startup_scripts/mmm5-tax-day/fri-uids.txt"
+    )
+    uids = load_uids(path)
+    agent.tell_agent_by_uid(uids)
+
+
+@shutdown_decorator
+def shutdown_agent():
+    return agent.stop()
+
+
+register_variable("Told UIDs", agent, "tell_cache")
+register_variable("Agent Name", agent, "instance_name")
diff --git a/bmm_agents/startup_scripts/mmm5-tax-day/Pt_KmeansMonarch.py b/bmm_agents/startup_scripts/mmm5-tax-day/Pt_KmeansMonarch.py
@@ -38,34 +38,48 @@
     subject_qserver=pdf_objects["qserver"],
     subject_kafka_producer=pdf_objects["kafka_producer"],
     subject_endstation_key="pdf",
-    pdf_origin=(17.574, 4.075),
+    pdf_origin=(-128.85, 49.91),
     # Active Kmeans Args
-    bounds=np.array([(-31, 31), (-31, 31)]),
+    bounds=np.array([(-30, 30), (-30, 30)]),
     # BS Adaptive Args
     ask_on_tell=False,
     report_on_tell=True,
-    k_clusters=6,
+    k_clusters=4,
     analyzed_element="Pt",
     queue_add_position="back",
     **beamline_objects
 )
 
 
-@startup_decorator
-def startup():
-    agent.start()
-    path = "/nsls2/data/bmm/shared/config/source/bmm-agents/bmm_agents/startup_scripts/historical_mmm4_uids.txt"
+def load_uids(path):
     with open(path, "r") as f:
         uids = []
         for line in f:
             uid = line.strip().strip(",").strip("'")
             if agent.trigger_condition(uid):
                 uids.append(uid)
+    return uids
+
+
+@startup_decorator
+def startup():
+    agent.start()
+    path = (
+        "/nsls2/data/bmm/shared/config/source/bmm-agents/"
+        "bmm_agents/startup_scripts/mmm5-tax-day/historical_mmm4_uids.txt"
+    )
+    uids = load_uids(path)
 
     agent.element_origins = old_mmm4_origin
     agent.tell_agent_by_uid(uids)
     agent.element_origins = new_mmm5_origin
 
+    path = (
+        "/nsls2/data/bmm/shared/config/source/bmm-agents/" "bmm_agents/startup_scripts/mmm5-tax-day/fri-uids.txt"
+    )
+    uids = load_uids(path)
+    agent.tell_agent_by_uid(uids)
+
 
 @shutdown_decorator
 def shutdown_agent():

diff --git a/bmm_agents/startup_scripts/mmm5-tax-day/Pt_kmeans.py b/bmm_agents/startup_scripts/mmm5-tax-day/Pt_kmeans.py
@@ -37,21 +37,30 @@
 )
 
 
-@startup_decorator
-def startup():
-    agent.start()
-    path = "/nsls2/data/bmm/shared/config/source/bmm-agents/bmm_agents/startup_scripts/historical_mmm4_uids.txt"
+def load_uids(path):
     with open(path, "r") as f:
         uids = []
         for line in f:
             uid = line.strip().strip(",").strip("'")
             if agent.trigger_condition(uid):
                 uids.append(uid)
+    return uids
+
+
+@startup_decorator
+def startup():
+    agent.start()
+    path = "/nsls2/data/bmm/shared/config/source/bmm-agents/bmm_agents/startup_scripts/historical_mmm4_uids.txt"
+    uids = load_uids(path)
 
     agent.element_origins = old_mmm4_origin
     agent.tell_agent_by_uid(uids)
     agent.element_origins = new_mmm5_origin
 
+    path = "/nsls2/data/bmm/shared/config/source/bmm-agents/bmm_agents/startup_scripts/mmm5-tax-day/fri-uids.txt"
+    uids = load_uids(path)
+    agent.tell_agent_by_uid(uids)
+
 
 @shutdown_decorator
 def shutdown_agent():

diff --git a/bmm_agents/startup_scripts/mmm5-tax-day/fri-uids.txt b/bmm_agents/startup_scripts/mmm5-tax-day/fri-uids.txt
@@ -0,0 +1,60 @@
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diff --git a/bmm_agents/startup_scripts/mmm5-tax-day/historical_mmm4_uids.txt b/bmm_agents/startup_scripts/mmm5-tax-day/historical_mmm4_uids.txt
@@ -0,0 +1,35 @@
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